From f51a5f6d9f3091e744b5433cd46f176e792520eb Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 4 Mar 2026 10:21:49 +0100 Subject: [PATCH 01/90] Bump version to 3.1.0dev --- .nf-core.yml | 2 +- CHANGELOG.md | 2 ++ nextflow.config | 2 +- ro-crate-metadata.json | 36 ++++++++++++++++++------------------ tests/pna.nf.test.snap | 4 ++-- 5 files changed, 24 insertions(+), 22 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 76c9d634..56786765 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -23,4 +23,4 @@ template: - fastqc - multiqc - igenomes - version: 3.0.0 + version: 3.1.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 66c046ee..9ab14961 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev - xxxx-xx-xx + ## [[3.0.0](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-02-23 ### Changed diff --git a/nextflow.config b/nextflow.config index bf37d4d8..9173b26f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -357,7 +357,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.04.0' - version = '3.0.0' + version = '3.1.0dev' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 22cf3cd8..19d79d01 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-02-23T07:30:51+00:00", - "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details):\n\n`samplesheet.csv`:\n\n```csv\nsample,sample_alias,condition,design,panel,fastq_1,fastq_2\nsample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-03-04T09:17:44+00:00", + "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details):\n\n`samplesheet.csv`:\n\n```csv\nsample,sample_alias,condition,design,panel,fastq_1,fastq_2\nsample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { "@id": "main.nf" @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#9f9abf50-29d2-4cd8-be9c-9f2623f36243" + "@id": "#bef5c60b-3d66-424d-8857-15f0e6de5e0b" } ], "name": "nf-core/pixelator" @@ -134,14 +134,14 @@ "@id": "https://orcid.org/0009-0006-0086-2470" }, { - "@id": "https://orcid.org/0000-0003-2702-1103" + "@id": "#johan.dahlberg@pixelgen.tech" }, { - "@id": "#johan.dahlberg@pixelgen.tech" + "@id": "https://orcid.org/0000-0003-2702-1103" } ], "dateCreated": "", - "dateModified": "2026-02-23T08:30:51Z", + "dateModified": "2026-03-04T10:17:44Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -175,10 +175,10 @@ }, "url": [ "https://github.com/nf-core/pixelator", - "https://nf-co.re/pixelator/3.0.0/" + "https://nf-co.re/pixelator/dev/" ], "version": [ - "3.0.0" + "3.1.0dev" ] }, { @@ -194,11 +194,11 @@ "version": "!>=25.04.0" }, { - "@id": "#9f9abf50-29d2-4cd8-be9c-9f2623f36243", + "@id": "#bef5c60b-3d66-424d-8857-15f0e6de5e0b", "@type": "TestSuite", "instance": [ { - "@id": "#941d74f8-288a-4b81-828b-bb4ed6d64d62" + "@id": "#2205d57e-47b7-4159-bcbf-aa4542dd042f" } ], "mainEntity": { @@ -207,7 +207,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#941d74f8-288a-4b81-828b-bb4ed6d64d62", + "@id": "#2205d57e-47b7-4159-bcbf-aa4542dd042f", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -346,17 +346,17 @@ "email": "florian.detemmerman@pixelgen.com", "name": "Florian De Temmerman" }, - { - "@id": "https://orcid.org/0000-0003-2702-1103", - "@type": "Person", - "email": "adrien.coulier@pixelgen.com", - "name": "Adrien Coulier" - }, { "@id": "#johan.dahlberg@pixelgen.tech", "@type": "Person", "email": "johan.dahlberg@pixelgen.tech", "name": "Johan Dahlberg" + }, + { + "@id": "https://orcid.org/0000-0003-2702-1103", + "@type": "Person", + "email": "adrien.coulier@pixelgen.com", + "name": "Adrien Coulier" } ] } \ No newline at end of file diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index 193c79bc..4ea6faca 100644 --- a/tests/pna.nf.test.snap +++ b/tests/pna.nf.test.snap @@ -109,7 +109,7 @@ "pixelator": "0.23.0" }, "Workflow": { - "nf-core/pixelator": "v3.0.0" + "nf-core/pixelator": "v3.1.0dev" } } ], @@ -154,7 +154,7 @@ "pixelator": "0.23.0" }, "Workflow": { - "nf-core/pixelator": "v3.0.0" + "nf-core/pixelator": "v3.1.0dev" } }, [ From 21b8d5efe83527303e71d59704fa0a93db6dc56c Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 08:36:41 +0100 Subject: [PATCH 02/90] Move container env vars to own config --- conf/container_env.config | 11 +++++++++++ nextflow.config | 24 ++++++------------------ 2 files changed, 17 insertions(+), 18 deletions(-) create mode 100644 conf/container_env.config diff --git a/conf/container_env.config b/conf/container_env.config new file mode 100644 index 00000000..b86610f4 --- /dev/null +++ b/conf/container_env.config @@ -0,0 +1,11 @@ +env { + MPLCONFIGDIR = '/tmp/.config/matplotlib' + NUMBA_CACHE_DIR = "/tmp/.numba_cache" + + // quarto needs a writeable cache directory + XDG_CACHE_HOME = "/tmp/.cache" + XDG_DATA_HOME = "/tmp/.data" + + // DuckDB temp directory when running in containers + PIXELATOR_DUCKDB_TEMP_DIR = "/tmp" +} diff --git a/nextflow.config b/nextflow.config index 9173b26f..e333874a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -129,18 +129,6 @@ params { // Load base.config by default for all pipelines includeConfig 'conf/base.config' -def container_env_options = [ - "MPLCONFIGDIR": '/tmp/.config/matplotlib', - "NUMBA_CACHE_DIR": "/tmp/.numba_cache", - - // quarto needs a writeable cache directory - "XDG_CACHE_HOME": "/tmp/.cache", - "XDG_DATA_HOME": "/tmp/.data", - - // DuckDB temp directory when running in containers - "PIXELATOR_DUCKDB_TEMP_DIR": "/tmp", -] - profiles { debug { dumpHashes = true @@ -177,7 +165,7 @@ profiles { charliecloud.enabled = false apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' - env = container_env_options + includeConfig 'conf/container_env.config' } arm64 { process.arch = 'arm64' @@ -202,7 +190,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - env = container_env_options + includeConfig 'conf/container_env.config' } podman { podman.enabled = true @@ -213,7 +201,7 @@ profiles { charliecloud.enabled = false apptainer.enabled = false podman.runOptions = '--userns=keep-id' - env = container_env_options + includeConfig 'conf/container_env.config' } shifter { shifter.enabled = true @@ -223,7 +211,7 @@ profiles { podman.enabled = false charliecloud.enabled = false apptainer.enabled = false - env = container_env_options + includeConfig 'conf/container_env.config' } charliecloud { charliecloud.enabled = true @@ -233,7 +221,7 @@ profiles { podman.enabled = false shifter.enabled = false apptainer.enabled = false - env = container_env_options + includeConfig 'conf/container_env.config' } apptainer { apptainer.enabled = true @@ -244,7 +232,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - env = container_env_options + includeConfig 'conf/container_env.config' } wave { apptainer.ociAutoPull = true From ef4f36bff2a4add3fe3034527d58b3ba4d8c73a4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 08:45:31 +0100 Subject: [PATCH 03/90] Remove `samplesheet_sha` As far as I understand, this was set so that Nextflow would re-run in case the samplesheet changes. Nextflow does this natively though --- workflows/pixelator.nf | 5 ----- 1 file changed, 5 deletions(-) diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index 72378ca3..2fdb6bf2 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -8,11 +8,6 @@ include { paramsSummaryMap } from 'plugin/nf-schema' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pixelator_pipeline' -// Inject the samplesheet SHA-1 into the params object -if (params.input) { - params.samplesheet_sha = file(params.input).bytes.digest('sha-1') -} - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES From 5291f1b65aa4f1217fe655efee835bd01aa34404 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 10:37:16 +0100 Subject: [PATCH 04/90] Fix implicit closures --- conf/modules.pna.config | 42 +++++++------------ .../local/pna/generate_reports/main.nf | 8 ++-- subworkflows/local/pna/main.nf | 9 ++-- .../utils_nfcore_pixelator_pipeline/main.nf | 6 +-- 4 files changed, 28 insertions(+), 37 deletions(-) diff --git a/conf/modules.pna.config b/conf/modules.pna.config index 5b601a94..4076e065 100644 --- a/conf/modules.pna.config +++ b/conf/modules.pna.config @@ -32,7 +32,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'amplicon/*.amplicon.fq.zst', - saveAs: { params.save_pna_amplicon_reads || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_amplicon_reads || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -43,7 +43,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } @@ -62,19 +62,19 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'demux/*.parquet', - saveAs: { params.save_pna_demux_parquet || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_demux_parquet || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'demux/*.demux.passed.fq.zst', - saveAs: { params.save_pna_demux_passed_reads || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_demux_passed_reads || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'demux/*.demux.failed.fq.zst', - saveAs: { params.save_pna_demux_failed_reads || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_demux_failed_reads || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -85,7 +85,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } @@ -102,7 +102,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'collapse/*.parquet', - saveAs: { params.save_pna_collapsed_reads || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_collapsed_reads || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -113,7 +113,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } @@ -141,7 +141,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'graph/*.pxl', - saveAs: { params.save_pna_graph_pixelfile || params.save_all ? it : null }, + saveAs: { filename -> params.save_pna_graph_pixelfile || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -152,7 +152,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } @@ -171,12 +171,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'denoise/*.pxl', - saveAs: { - if (params.save_pna_denoise_pixelfile) { - return it - } - return null - }, + saveAs: { filename -> params.save_pna_denoise_pixelfile ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -187,7 +182,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json ? it : null }, + saveAs: { filename -> params.save_json ? filename : null }, ], ] } @@ -210,12 +205,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: 'analysis/*.pxl', - saveAs: { - if (params.save_pna_analysis_pixelfile || params.save_all) { - return it - } - return null - }, + saveAs: { filename -> params.save_pna_analysis_pixelfile || params.save_all ? filename : null }, ], [ path: { "${params.outdir}/pixelator/logs/${meta.id}" }, @@ -226,7 +216,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } @@ -248,7 +238,7 @@ process { pattern: 'layout/*.pxl', saveAs: { // Trim the annotate directory prefix from the output name - new File(it).name + filename -> new File(filename).name }, ], [ @@ -260,7 +250,7 @@ process { path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, pattern: '**/*.{report,meta}.json', - saveAs: { params.save_json || params.save_all ? it : null }, + saveAs: { filename -> params.save_json || params.save_all ? filename : null }, ], ] } diff --git a/subworkflows/local/pna/generate_reports/main.nf b/subworkflows/local/pna/generate_reports/main.nf index 7b6306bd..92198906 100644 --- a/subworkflows/local/pna/generate_reports/main.nf +++ b/subworkflows/local/pna/generate_reports/main.nf @@ -32,9 +32,9 @@ workflow PNA_GENERATE_REPORTS { .groupTuple() .map { id, data -> if (data instanceof List) { - def newMeta = [:] - data.each { newMeta += it } - return [id, newMeta] + def combined_meta = [:] + data.each { meta -> combined_meta += meta } + return [id, combined_meta] } return [id, data] } @@ -86,7 +86,7 @@ workflow PNA_GENERATE_REPORTS { EXPERIMENT_SUMMARY ( samplesheet, ch_grouped_data ) ch_experiment_summary = EXPERIMENT_SUMMARY.out.html } else { - ch_experiment_summary = ch_grouped_data.map { it -> it[0] }.combine(Channel.of([])) + ch_experiment_summary = ch_grouped_data.map { it -> it[0] }.combine(channel.of([])) } diff --git a/subworkflows/local/pna/main.nf b/subworkflows/local/pna/main.nf index 06720552..f71e467b 100644 --- a/subworkflows/local/pna/main.nf +++ b/subworkflows/local/pna/main.nf @@ -105,14 +105,15 @@ workflow PNA { newMeta.remove('parts') // Strip the duplicates meta from each element - def parquet = data.collect { it[1] }.flatten() - def reports = data.collect { it[2] }.flatten() + def parquet = data.collect { _meta, collapsed, _reports -> collapsed }.flatten() + def reports = data.collect { _meta, _collapsed, reports -> reports }.flatten() [newMeta, parquet, reports] } ch_collapse_combine_split = ch_collapse_collected.branch { - single: it[1].size() == 1 - multi: it[1].size() > 1 + _meta, parquet, _reports -> + single: parquet.size() == 1 + multi: parquet.size() > 1 } diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 805172af..2600dbfe 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -120,7 +120,7 @@ workflow PIPELINE_INITIALISATION { ch_input = channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { - validate_input_samplesheet(inputBaseDir, it) + row -> validate_input_samplesheet(inputBaseDir, row) } // @@ -131,13 +131,13 @@ workflow PIPELINE_INITIALISATION { // Create a set of valid pixelator options to pass to --design ch_design_options = PIXELATOR_LIST_OPTIONS.out.designs .splitText() - .map { it.trim() } + .map { design_option -> design_option.trim() } .reduce(new HashSet()) { prev, curr -> prev << curr } // Create a set of valid pixelator panel keys to pass using --panel ch_panel_options = PIXELATOR_LIST_OPTIONS.out.panels .splitText() - .map { it.trim() } + .map { panel_option -> panel_option.trim() } .reduce(new HashSet()) { prev, curr -> prev << curr } From 26193f3482afbbdd3a219d041866addbecafcdde Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 10:39:04 +0100 Subject: [PATCH 05/90] Fix unused parameters --- .../local/pixelator/single-cell-pna/amplicon/main.nf | 3 +-- subworkflows/local/pna/main.nf | 2 +- .../local/utils_nfcore_pixelator_pipeline/main.nf | 6 +++--- workflows/pixelator.nf | 10 +++++----- 4 files changed, 10 insertions(+), 11 deletions(-) diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/single-cell-pna/amplicon/main.nf index ef0231c0..e1ec72fd 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/main.nf +++ b/modules/local/pixelator/single-cell-pna/amplicon/main.nf @@ -25,7 +25,6 @@ process PIXELATOR_PNA_AMPLICON { script: def prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: '' - def r = reads // Make list of old name and new name pairs to use for renaming // Use R1/R2 style suffixes for limited backward compatibility with pixelator<0.17 @@ -34,7 +33,7 @@ process PIXELATOR_PNA_AMPLICON { : reads.withIndex().collect { entry, index -> [entry, "${prefix}_R${index + 1}${getFileSuffix(entry)}"] }) // Flatten a list of tuples into a single string joined with spaces def rename_to = old_new_pairs.flatten().join(' ') - def renamed_reads = old_new_pairs.collect { old_name, new_name -> new_name }.join(' ') + def renamed_reads = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ') """ diff --git a/subworkflows/local/pna/main.nf b/subworkflows/local/pna/main.nf index f71e467b..90b37813 100644 --- a/subworkflows/local/pna/main.nf +++ b/subworkflows/local/pna/main.nf @@ -175,7 +175,7 @@ workflow PNA { .groupTuple(size: 2) - ch_input = Channel.fromPath(params.input) + ch_input = channel.fromPath(params.input) PNA_GENERATE_REPORTS( ch_input, diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 2600dbfe..8ba3928e 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -30,7 +30,7 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - monochrome_logs // boolean: Do not use coloured log outputs + _monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet @@ -324,7 +324,7 @@ def resolve_relative_path(relative_path, URI samplesheet_path) { try { uri = new URI(relative_path) } - catch (URISyntaxException exc) { + catch (URISyntaxException _exc) { return relative_path } @@ -394,7 +394,7 @@ def get_data_basedir(URI samplesheet, String input_basedir) { try { uri = new URI(input_basedir) } - catch (URISyntaxException exc) { + catch (URISyntaxException _exc) { return samplesheet } diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index 2fdb6bf2..68e34b72 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -61,8 +61,8 @@ workflow PIXELATOR { // // Split the samplesheet channel in reads and panel_files // - ch_reads = ch_samplesheet.map { meta, panel, reads -> [ meta, reads ] } - ch_panel_files = ch_samplesheet.map { meta, panel, reads -> [ meta, panel ] } + ch_reads = ch_samplesheet.map { meta, _panel, reads -> [ meta, reads ] } + ch_panel_files = ch_samplesheet.map { meta, panel, _reads -> [ meta, panel ] } ch_fastq_split = ch_reads .groupTuple() @@ -99,9 +99,9 @@ workflow PIXELATOR { } ch_cat_panel_files = ch_cat_fastq - .map { meta, _ -> [meta.id, meta] } + .map { meta, _fastqs -> [meta.id, meta] } .join(ch_checked_panel_files) - .map { id, meta, panel_files -> [meta, panel_files] } + .map { _id, meta, panel_files -> [meta, panel_files] } ch_fastq_technology_split = ch_cat_fastq .branch { @@ -149,7 +149,7 @@ workflow PIXELATOR { name: 'nf_core_' + 'pixelator_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true - ).set { ch_collated_versions } + ) emit: versions = ch_versions // channel: [ path(versions.yml) ] From 061edaa6c685ee08eb7939b7d6cb7b37b0d8bfae Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 10:55:57 +0100 Subject: [PATCH 06/90] Update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f6def66b..c5fc5ed6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev - xxxx-xx-xx +### Enhancements & fixes + +- Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) + ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 ### Enhancements & fixes From 3b75dc01ff5c5cf6b5ba073ce71ac8a8d5bcc929 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 12:56:46 +0100 Subject: [PATCH 07/90] Standardize option group titles --- nextflow_schema.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d0fac578..41aeb12c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -45,7 +45,7 @@ } }, "pna_amplicon_options": { - "title": "Amplicon generation options", + "title": "Amplicon options", "type": "object", "fa_icon": "fas fa-circle", "properties": { @@ -108,7 +108,7 @@ } }, "pna_demux_options": { - "title": "Demux options for PNA data", + "title": "Demux options", "type": "object", "properties": { "pna_demux_mismatches": { @@ -192,7 +192,7 @@ } }, "pna_graph_options": { - "title": "Options for pixelator graph command on PNA data.", + "title": "Graph options", "type": "object", "properties": { "save_pna_graph_pixelfile": { @@ -281,7 +281,7 @@ } }, "pna_denoise_options": { - "title": "Options for pixelator denoise command.", + "title": "Denoise options", "type": "object", "properties": { "skip_denoise": { @@ -314,7 +314,7 @@ } }, "pna_analysis_options": { - "title": "Options for pixelator analysis command.", + "title": "Analysis options", "type": "object", "properties": { "skip_analysis": { @@ -358,7 +358,7 @@ } }, "pna_layout_options": { - "title": "Options for pixelator single-cell-pna layout command.", + "title": "Layout options", "type": "object", "properties": { "skip_layout": { @@ -391,7 +391,7 @@ } }, "experiment_summary_options": { - "title": "Options for experiment summary.", + "title": "Experiment Summary options", "type": "object", "properties": { "skip_experiment_summary": { From 0c1c06114932ec1bc204307881893a16a46299e5 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 15:19:02 +0100 Subject: [PATCH 08/90] Use $TMPDIR to set temporaryr directories --- conf/container_env.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/container_env.config b/conf/container_env.config index b86610f4..9a1de411 100644 --- a/conf/container_env.config +++ b/conf/container_env.config @@ -1,11 +1,11 @@ env { - MPLCONFIGDIR = '/tmp/.config/matplotlib' - NUMBA_CACHE_DIR = "/tmp/.numba_cache" + MPLCONFIGDIR = '${TMPDIR:-/tmp}/.config/matplotlib' + NUMBA_CACHE_DIR = '${TMPDIR:-/tmp}/.numba_cache' // quarto needs a writeable cache directory - XDG_CACHE_HOME = "/tmp/.cache" - XDG_DATA_HOME = "/tmp/.data" + XDG_CACHE_HOME = '${TMPDIR:-/tmp}/.cache' + XDG_DATA_HOME = '${TMPDIR:-/tmp}/.data' // DuckDB temp directory when running in containers - PIXELATOR_DUCKDB_TEMP_DIR = "/tmp" + PIXELATOR_DUCKDB_TEMP_DIR = '${TMPDIR:-/tmp}' } From ef23b1dd7a72dceb0631ca7796931d3440f26b1e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 15:30:31 +0100 Subject: [PATCH 09/90] Add `container_env.config` to nf-test triggers --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index d84fa287..aa1dc683 100644 --- a/nf-test.config +++ b/nf-test.config @@ -15,7 +15,7 @@ config { profile "test" // list of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore', 'assets/schema_input.json', 'nextflow_schema.json' + triggers 'nextflow.config', 'conf/container_env.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore', 'assets/schema_input.json', 'nextflow_schema.json' // load the necessary plugins plugins { From 044bd48c467b8f094acf5e202040007f660362ef Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 15:34:01 +0100 Subject: [PATCH 10/90] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5fc5ed6..e5cfae67 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes - Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) +- Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 From f1c38bc8520bca29bac310801223dee7c5876db6 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 16 Mar 2026 15:47:33 +0100 Subject: [PATCH 11/90] Add note describing how TMPDIR can be used --- docs/usage.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 1c1e05c2..68c80dee 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -178,6 +178,9 @@ You can find an extensive example of a `params.yaml` file with all options and documentation in comments [here](../assets/params-file.yml). You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). +> [!NOTE] +> By default, processes from nf-core/pixelator will the path defined in `TMPDIR` to store temporary file. If this variable is not defined, they will fallback to `/tmp`. + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: From 0fc8d857d2fd8d3364119c7a0d6f50c2c6c46b45 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 17 Mar 2026 09:32:49 +0100 Subject: [PATCH 12/90] Update docs/usage.md Co-authored-by: Johan Dahlberg --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 68c80dee..6e3fef34 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -179,7 +179,7 @@ documentation in comments [here](../assets/params-file.yml). You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). > [!NOTE] -> By default, processes from nf-core/pixelator will the path defined in `TMPDIR` to store temporary file. If this variable is not defined, they will fallback to `/tmp`. +> By default, processes from nf-core/pixelator will use the path defined in `TMPDIR` to store temporary file. If this variable is not defined, they will fallback to `/tmp`. ### Updating the pipeline From bcdb527579b0b80d6da0965459264361aaaf618a Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 30 Mar 2026 15:11:37 +0200 Subject: [PATCH 13/90] Enable retry for experiment summary --- modules/local/experiment_summary/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index 2967a5c1..d2e8fbee 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -1,6 +1,7 @@ process EXPERIMENT_SUMMARY { tag "${meta.id}" label "process_medium" + label "error_retry" container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'quay.io/pixelgen-technologies/pixelatores:0.6.0' From e3e584d3d254a66d448c9bfb186837c7f42012f9 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 30 Mar 2026 15:50:24 +0200 Subject: [PATCH 14/90] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e5cfae67..11cb78b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) +- Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 From 86152997b31768d071abced0aa2a677b475e6359 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Apr 2026 14:40:19 +0200 Subject: [PATCH 15/90] Update pixelatorES to 0.8.6 --- modules/local/experiment_summary/main.nf | 4 ++-- modules/local/experiment_summary/tests/main.nf.test.snap | 6 +++--- tests/pna.nf.test.snap | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index d2e8fbee..e426544f 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -4,8 +4,8 @@ process EXPERIMENT_SUMMARY { label "error_retry" container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelatores:0.6.0' - : 'quay.io/pixelgen-technologies/pixelatores:0.6.0'}" + ? 'quay.io/pixelgen-technologies/pixelatores:0.8.6' + : 'quay.io/pixelgen-technologies/pixelatores:0.8.6'}" input: path samplesheet_path diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index a2a7cec2..0fb5fb0b 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -10,7 +10,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.6.0 " + "0.8.6 " ] ] ], @@ -26,7 +26,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.6.0 " + "0.8.6 " ] ] ], @@ -36,4 +36,4 @@ }, "timestamp": "2025-12-11T13:57:21.610883862" } -} \ No newline at end of file +} diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index 5b9d162d..a97d4339 100644 --- a/tests/pna.nf.test.snap +++ b/tests/pna.nf.test.snap @@ -79,7 +79,7 @@ ], { "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.6.0" + "experiment-summary": "0.8.6" }, "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.23.0" @@ -124,7 +124,7 @@ 20, { "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.6.0" + "experiment-summary": "0.8.6" }, "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.23.0" From 46f9a25aa74ef198cf61290a54eea72a4d1948d6 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Apr 2026 14:42:03 +0200 Subject: [PATCH 16/90] Update changelog --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 11cb78b7..d3e6dbd9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) +- Updated pixelatorES to 0.6.0 in PNA experiment summary step by @Arazt [#197](https://github.com/nf-core/pixelator/pull/197) + +### Software dependencies + +| Dependency | Old version | New version | +| ------------- | ----------- | ----------- | +| `pixelatorES` | 0.6.0 | 0.8.6 | ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 From e445087c649ce81e357352c40ab75905948faafb Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Apr 2026 14:46:56 +0200 Subject: [PATCH 17/90] Fix typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3e6dbd9..3de29736 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) -- Updated pixelatorES to 0.6.0 in PNA experiment summary step by @Arazt [#197](https://github.com/nf-core/pixelator/pull/197) +- Updated pixelatorES to 0.6.0 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197) ### Software dependencies From 48195cd932bca7dff366b8a1a60899215fb0bba1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 28 Apr 2026 11:21:33 +0000 Subject: [PATCH 18/90] Template update for nf-core/tools version 4.0.0 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 123 ------------ .github/PULL_REQUEST_TEMPLATE.md | 4 +- .github/actions/get-shards/action.yml | 2 +- .github/actions/nf-test/action.yml | 10 +- .github/workflows/awsfulltest.yml | 25 ++- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 14 +- .github/workflows/fix_linting.yml | 22 +-- .github/workflows/linting.yml | 34 ++-- .github/workflows/linting_comment.yml | 4 +- .github/workflows/nf-test.yml | 8 +- .github/workflows/release-announcements.yml | 4 +- .../workflows/template-version-comment.yml | 6 +- .gitignore | 1 + .nf-core.yml | 7 +- .pre-commit-config.yaml | 16 +- .prettierignore | 2 - CHANGELOG.md | 2 +- README.md | 12 +- assets/adaptivecard.json | 67 ------- assets/email_template.html | 2 +- assets/slackreport.json | 34 ---- conf/base.config | 2 +- docs/CONTRIBUTING.md | 182 ++++++++++++++++++ docs/usage.md | 8 +- main.nf | 4 +- modules.json | 4 +- nextflow.config | 12 +- nextflow_schema.json | 9 +- nf-test.config | 26 ++- ro-crate-metadata.json | 31 ++- .../utils_nfcore_pixelator_pipeline/main.nf | 17 +- .../nf-core/utils_nfcore_pipeline/main.nf | 66 +------ .../utils_nfcore_pipeline/tests/main.nf.test | 29 +++ .../tests/main.nf.test.snap | 19 ++ .../nf-core/utils_nfschema_plugin/main.nf | 3 +- .../tests/nextflow.config | 2 +- tests/default.nf.test | 14 +- tests/nextflow.config | 2 +- workflows/pixelator.nf | 15 +- 43 files changed, 414 insertions(+), 439 deletions(-) delete mode 100644 .github/CONTRIBUTING.md delete mode 100644 assets/adaptivecard.json delete mode 100644 assets/slackreport.json create mode 100644 docs/CONTRIBUTING.md create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 97c8c97f..237c9ed0 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,4 +1,5 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", "image": "nfcore/devcontainer:latest", diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 08165cfd..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,123 +0,0 @@ -# `nf-core/pixelator`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/pixelator. - -We try to manage the required tasks for nf-core/pixelator using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/pixelator then the best place to ask is on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/pixelator, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/pixelator issues](https://github.com/nf-core/pixelator/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/pixelator repository](https://github.com/nf-core/pixelator) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Getting help - -For further information/help, please consult the [nf-core/pixelator documentation](https://nf-co.re/pixelator/usage) and don't hesitate to get in touch on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the `nf-core/pixelator` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/pixelator/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 3e33e429..a302e7a5 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pixelator/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pixelator/tree/master/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pixelator/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pixelator/tree/master/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/pixelator _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index 34085279..e2833ee9 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c7..ad686e8e 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@main + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -48,7 +48,7 @@ runs: - name: Conda setup if: contains(inputs.profile, 'conda') - uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 with: auto-update-conda: true conda-solver: libmamba diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8eca4a89..16329933 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -23,7 +23,7 @@ jobs: echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -33,14 +33,33 @@ jobs: compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/pixelator/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'pixelator' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *pixelator/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *pixelator/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/pixelator/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index c0673dcd..9d2d7367 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Seqera Platform CLI tool action - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 0e3d6360..758348db 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -21,7 +21,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 with: message: | ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 6adb0fff..172de6f3 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 + - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 45884ff9..5b6592c1 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,12 +39,12 @@ jobs: needs: configure steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" @@ -54,10 +54,16 @@ jobs: with: apptainer-version: 1.3.4 + - name: Read .nf-core.yml + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Make a cache directory for the container images run: | @@ -127,7 +133,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index daaecce6..64bb55d1 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -31,22 +31,18 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' + if: steps.prek.outcome == 'success' uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} @@ -54,7 +50,7 @@ jobs: - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7a527a34..bfe46c98 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,33 +11,31 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - - name: Set up Python 3.14 - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml @@ -45,12 +43,10 @@ jobs: config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' }} + if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -58,7 +54,7 @@ jobs: run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Run nf-core pipelines lint --release - if: ${{ github.base_ref == 'master' }} + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -71,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index e6e9bc26..2bc3c07f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 + uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 + uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c98d76ec..efd72d65 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -18,7 +18,7 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.3" + NFT_VER: "0.9.4" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.04.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 431d3d44..78d5dbe0 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -18,7 +18,7 @@ jobs: id: get_description run: | echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -34,7 +34,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index e8560fc7..ea30827e 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: ref: ${{ github.event.pull_request.head.sha }} @@ -29,7 +29,7 @@ jobs: run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 if: | contains(env.OUTPUT, 'nf-core') with: @@ -42,5 +42,5 @@ jobs: > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. > Please update your pipeline to the latest version. > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). # diff --git a/.gitignore b/.gitignore index a42ce016..cc2b1a77 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc null/ +.lineage/ diff --git a/.nf-core.yml b/.nf-core.yml index d99daff0..2fdb49a0 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -3,16 +3,17 @@ lint: - assets/multiqc_config.yml - conf/igenomes.config - conf/igenomes_ignored.config + - conf/test.config - tests/default.nf.test files_unchanged: - assets/nf-core-pixelator_logo_light.png - .github/PULL_REQUEST_TEMPLATE.md multiqc_config: false -nf_core_version: 3.5.1 +nf_core_version: 4.0.0 repository_type: pipeline template: author: Pixelgen Technologies AB - description: Pipeline for analysis of Molecular Pixelation assays + description: Pipeline for analysis of Proximity Network Assay data force: false is_nfcore: true name: pixelator @@ -22,4 +23,4 @@ template: - fastqc - multiqc - igenomes - version: 2.3.0dev + version: 3.1.0dev diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d06777a8..f51e1a28 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.6.2 + - prettier@3.8.3 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -13,15 +13,21 @@ repos: exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ - id: end-of-file-fixer exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] diff --git a/.prettierignore b/.prettierignore index dd749d43..63cde500 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 36f09056..b89b7bc9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.3.0dev - [date] +## v3.1.0dev - [date] Initial release of nf-core/pixelator, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 50939e58..7d2819a0 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -30,13 +30,13 @@ --> + workflows use the "tube map" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples. --> ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. diff --git a/docs/usage.md b/docs/usage.md index 2733c35a..6cf29d81 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -76,7 +76,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > [!WARNING] -> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -172,19 +172,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/main.nf b/main.nf index 0835e2e4..3491870b 100644 --- a/main.nf +++ b/main.nf @@ -38,7 +38,8 @@ workflow NFCORE_PIXELATOR { // WORKFLOW: Run pipeline // PIXELATOR ( - samplesheet + samplesheet, + params.outdir, ) } /* @@ -80,7 +81,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, ) } diff --git a/modules.json b/modules.json index 1019d574..944f91ac 100644 --- a/modules.json +++ b/modules.json @@ -15,12 +15,12 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", + "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", "installed_by": ["subworkflows"] } } diff --git a/nextflow.config b/nextflow.config index 05684380..6ae4769d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,7 +20,6 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false @@ -41,6 +40,10 @@ params { validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -235,11 +238,11 @@ manifest { ], ] homePage = 'https://github.com/nf-core/pixelator' - description = """Pipeline for analysis of Molecular Pixelation assays""" + description = """Pipeline for analysis of Proximity Network Assay data""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=25.04.0' - version = '2.3.0dev' + nextflowVersion = '!>=25.10.4' + version = '3.1.0dev' doi = '' } @@ -252,6 +255,5 @@ validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } - // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 5dd3aac9..c8e370a9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/pixelator/master/nextflow_schema.json", "title": "nf-core/pixelator pipeline parameters", - "description": "Pipeline for analysis of Molecular Pixelation assays", + "description": "Pipeline for analysis of Proximity Network Assay data", "type": "object", "$defs": { "input_output_options": { @@ -128,13 +128,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", diff --git a/nf-test.config b/nf-test.config index 3a1fff59..f7aaeb4a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,21 +1,35 @@ config { // location for all nf-test tests - testsDir "." + testsDir = "." // nf-test directory including temporary files for each test - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "tests/nextflow.config" + configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] // run all test with defined profile(s) from the main nextflow.config - profile "test" + profile = "test" // list of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] // load the necessary plugins plugins { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index ae2dfb20..bbf8930a 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-11-20T09:31:50+00:00", - "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written by Pixelgen Technologies AB.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-28T11:21:26+00:00", + "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written by Pixelgen Technologies AB.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#d5872455-752b-47d2-9520-1694b7eda989" + "@id": "#acca1f97-4f8e-4da7-bda8-3b0a4e76525a" } ], "name": "nf-core/pixelator" @@ -106,7 +106,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -116,13 +116,13 @@ { "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], - "creator": [ + "contributor": [ { - "@id": "https://orcid.org/0009-0006-0086-2470" + "@id": "#fd2bba62-3db0-4a3d-a2db-e27f8cf4a960" } ], "dateCreated": "", - "dateModified": "2025-11-20T09:31:50Z", + "dateModified": "2026-04-28T11:21:26Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -143,7 +143,7 @@ "@id": "https://nf-co.re/" }, "url": ["https://github.com/nf-core/pixelator", "https://nf-co.re/pixelator/dev/"], - "version": ["2.3.0dev"] + "version": ["3.1.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -155,14 +155,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.10.4" }, { - "@id": "#d5872455-752b-47d2-9520-1694b7eda989", + "@id": "#acca1f97-4f8e-4da7-bda8-3b0a4e76525a", "@type": "TestSuite", "instance": [ { - "@id": "#ec7331a4-5ae0-439a-a031-1bb0344f738e" + "@id": "#43f668b2-9ddd-437b-8b85-a3b175e31f3f" } ], "mainEntity": { @@ -171,7 +171,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#ec7331a4-5ae0-439a-a031-1bb0344f738e", + "@id": "#43f668b2-9ddd-437b-8b85-a3b175e31f3f", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -290,10 +290,9 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0009-0006-0086-2470", + "@id": "#fd2bba62-3db0-4a3d-a2db-e27f8cf4a960", "@type": "Person", - "email": "florian.detemmerman@pixelgen.com", - "name": "Florian De Temmerman" + "name": "Pixelgen Technologies AB" } ] } diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index dd217def..3b78276c 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -14,7 +14,6 @@ include { samplesheetToList } from 'plugin/nf-schema' include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -54,6 +53,9 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + + def before_text = "" + def after_text = "" before_text = """ -\033[2m----------------------------------------------------\033[0m- \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m @@ -71,6 +73,10 @@ workflow PIPELINE_INITIALISATION { * Software dependencies https://github.com/nf-core/pixelator/blob/master/CITATIONS.md """ + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFSCHEMA_PLUGIN ( @@ -97,7 +103,7 @@ workflow PIPELINE_INITIALISATION { // channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -135,7 +141,6 @@ workflow PIPELINE_COMPLETION { plaintext_email // boolean: Send plain-text email instead of HTML outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") @@ -157,13 +162,11 @@ workflow PIPELINE_COMPLETION { } completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } + } workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 2f30e9a4..afca5439 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /* @@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) { log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection() - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) - } -} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap new file mode 100644 index 00000000..859d1030 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8..1df8b76f 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + (params.help instanceof String && params.help != "true") ? params.help : "", ) exit 0 } @@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN { emit: dummy_emit = true } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 8d8c7371..f6537cc3 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.5.1" + id "nf-schema@2.6.1" } validation { diff --git a/tests/default.nf.test b/tests/default.nf.test index 842ef89f..f2bedc30 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,19 +13,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assert workflow.success assertAll( - { assert workflow.success}, { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_mqc_versions.yml"), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/nextflow.config b/tests/nextflow.config index a90f4366..728905dd 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,7 @@ // Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pixelator' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pixelator/' } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index d8faf39a..f724814b 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -17,14 +17,16 @@ workflow PIXELATOR { take: ch_samplesheet // channel: samplesheet read in from --input + outdir + main: - ch_versions = channel.empty() + def ch_versions = channel.empty() // // Collate and save software versions // - def topic_versions = Channel.topic("versions") + def topic_versions = channel.topic("versions") .distinct() .branch { entry -> versions_file: entry instanceof Path @@ -41,19 +43,16 @@ workflow PIXELATOR { "${process}:\n${tool_versions.join('\n')}" } - softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${params.outdir}/pipeline_info", + storeDir: "${outdir}/pipeline_info", name: 'nf_core_' + 'pixelator_software_' + 'versions.yml', sort: true, newLine: true - ).set { ch_collated_versions } - - + ) emit: versions = ch_versions // channel: [ path(versions.yml) ] - } /* From 2d1043e88e9d9f38dd9da445b85797af156db1bc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 30 Apr 2026 13:33:32 +0000 Subject: [PATCH 19/90] Template update for nf-core/tools version 4.0.2 --- .github/workflows/download_pipeline.yml | 8 +++++--- .github/workflows/fix_linting.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 2 +- README.md | 2 +- ro-crate-metadata.json | 18 +++++++++--------- 7 files changed, 19 insertions(+), 17 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 5b6592c1..a7bf4fc2 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -38,6 +38,9 @@ jobs: runs-on: ubuntu-latest needs: configure steps: + - name: Check out pipeline code + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - name: Install Nextflow uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 @@ -55,10 +58,9 @@ jobs: apptainer-version: 1.3.4 - name: Read .nf-core.yml - uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml - with: - config: ${{ github.workspace }}/.nf-core.yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" - name: Install dependencies run: | diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 64bb55d1..034b3453 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -37,7 +37,7 @@ jobs: # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfe46c98..8738ffc9 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -17,7 +17,7 @@ jobs: uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Run prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 nf-core: runs-on: ubuntu-latest diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 2bc3c07f..5b0c24f7 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index 2fdb49a0..3f4778bb 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ lint: - assets/nf-core-pixelator_logo_light.png - .github/PULL_REQUEST_TEMPLATE.md multiqc_config: false -nf_core_version: 4.0.0 +nf_core_version: 4.0.2 repository_type: pipeline template: author: Pixelgen Technologies AB diff --git a/README.md b/README.md index 7d2819a0..7a0bb2b6 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index bbf8930a..dd0262b0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2026-04-28T11:21:26+00:00", - "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written by Pixelgen Technologies AB.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-30T13:33:24+00:00", + "description": "

\n \n \n \"nf-core/pixelator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written by Pixelgen Technologies AB.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#acca1f97-4f8e-4da7-bda8-3b0a4e76525a" + "@id": "#ddc80f02-9b05-4a45-ab31-dc63c771cf54" } ], "name": "nf-core/pixelator" @@ -118,11 +118,11 @@ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "contributor": [ { - "@id": "#fd2bba62-3db0-4a3d-a2db-e27f8cf4a960" + "@id": "#64163091-7ca6-4faf-b8a3-b1611886b0a3" } ], "dateCreated": "", - "dateModified": "2026-04-28T11:21:26Z", + "dateModified": "2026-04-30T13:33:24Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -158,11 +158,11 @@ "version": "!>=25.10.4" }, { - "@id": "#acca1f97-4f8e-4da7-bda8-3b0a4e76525a", + "@id": "#ddc80f02-9b05-4a45-ab31-dc63c771cf54", "@type": "TestSuite", "instance": [ { - "@id": "#43f668b2-9ddd-437b-8b85-a3b175e31f3f" + "@id": "#1b901060-205b-49f1-914e-8aab057ad2cb" } ], "mainEntity": { @@ -171,7 +171,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#43f668b2-9ddd-437b-8b85-a3b175e31f3f", + "@id": "#1b901060-205b-49f1-914e-8aab057ad2cb", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -290,7 +290,7 @@ "url": "https://nf-co.re/" }, { - "@id": "#fd2bba62-3db0-4a3d-a2db-e27f8cf4a960", + "@id": "#64163091-7ca6-4faf-b8a3-b1611886b0a3", "@type": "Person", "name": "Pixelgen Technologies AB" } From 1b689e5e6f38f3ce5e426c404cd04beb3602d7cf Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 09:10:49 +0200 Subject: [PATCH 20/90] Update modules and subworkflows --- modules.json | 6 ++--- modules/nf-core/cat/fastq/main.nf | 2 +- .../utils_nfcore_pixelator_pipeline/main.nf | 3 ++- .../nf-core/utils_nextflow_pipeline/main.nf | 20 ++++++++++++---- .../tests/main.function.nf.test.snap | 6 ++--- .../nf-core/utils_nfschema_plugin/main.nf | 6 ++++- .../nf-core/utils_nfschema_plugin/meta.yml | 24 +++++++++++++++++++ .../utils_nfschema_plugin/tests/main.nf.test | 5 ++++ .../tests/nextflow.config | 2 +- 9 files changed, 60 insertions(+), 14 deletions(-) diff --git a/modules.json b/modules.json index ced907f4..75e0d8aa 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "cat/fastq": { "branch": "master", - "git_sha": "5d28ea7cfaebcfae6f74d1067ea766d8ff19dff3", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] } } @@ -16,7 +16,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -26,7 +26,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", + "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index e70af3d1..8d12a78c 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,7 +3,7 @@ process CAT_FASTQ { label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index baaa39ff..c7e54c3a 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -96,7 +96,8 @@ workflow PIPELINE_INITIALISATION { show_hidden, before_text, after_text, - command + command, + null, ) // diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index d6e593e8..37939acd 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -73,11 +73,23 @@ def getWorkflowVersion() { def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) + def temp_pf = workflow.launchDir.resolve(".${filename}") + def jsonGenerator = new groovy.json.JsonGenerator.Options() + .excludeNulls() + .addConverter(Path) { Path path -> path.toUriString() } + .addConverter(Duration) { Duration duration -> duration.toMillis() } + .addConverter(MemoryUnit) { MemoryUnit memory -> memory.toBytes() } + .addConverter(nextflow.script.types.VersionNumber) { nextflow.script.types.VersionNumber version -> version.toString() } + .build() + def jsonStr = jsonGenerator.toJson(params) temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - - nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + if (outdir instanceof Path) { + temp_pf.copyTo(outdir.resolve("pipeline_info/${filename}")) + } else if (outdir instanceof String) { + temp_pf.copyTo("${outdir}/pipeline_info/params_${timestamp}.json") + } else { + log.warn("Could not determine type of outdir, parameters JSON file will not be copied to output directory!") + } temp_pf.delete() } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index 25f2017f..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -4,10 +4,10 @@ "v9.9.9" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2025-06-26T13:20:08.944676306" + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 1df8b76f..0d9d4e0d 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { before_text // string: text to show before the help message and parameters summary after_text // string: text to show after the help message and parameters summary command // string: an example command of the pipeline + cli_typecast // boolean: whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour main: @@ -38,7 +39,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - (params.help instanceof String && params.help != "true") ? params.help : "", + (help instanceof String && help != "true") ? help : "", ) exit 0 } @@ -65,6 +66,9 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(parameters_schema) { validateOptions << [parametersSchema: parameters_schema] } + if(cli_typecast != null) { + validateOptions << [cliTypecast: cli_typecast] + } validateParameters(validateOptions) } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml index f7d9f028..1d8c75a9 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -25,6 +25,30 @@ input: option. When this input is empty it will automatically use the configured schema or "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way for meta pipelines. + - help: + type: boolean, string + description: | + Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message. + - help_full: + type: boolean + description: Show the full help message and exit. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - before_text: + type: string + description: Text to show before the parameters summary and help message. + - after_text: + type: string + description: Text to show after the parameters summary and help message. + - command: + type: string + description: An example command to run the pipeline, to show in the help message and the summary. + - cli_typecast: + type: boolean + description: | + Whether to apply typecasting to the parameters given via the CLI before validation. + Set this to `null` to use the default behavior. output: - dummy_emit: type: boolean diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index c977917a..1fd1eac1 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -63,6 +64,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -95,6 +97,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -127,6 +130,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -160,6 +164,7 @@ nextflow_workflow { input[6] = "Before" input[7] = "After" input[8] = "nextflow run test/test" + input[9] = null """ } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index f6537cc3..fd71cb8f 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.6.1" + id "nf-schema@2.7.2" } validation { From e500e221e5ff45fae6b1d22bda57af65d7818ce4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 09:25:46 +0200 Subject: [PATCH 21/90] Fix linting errors --- .nf-core.yml | 1 + main.nf | 1 - nextflow.config | 10 +++++++++- nf-test.config | 2 +- subworkflows/local/pna/main.nf | 1 - .../local/utils_nfcore_pixelator_pipeline/main.nf | 3 +-- workflows/pixelator.nf | 4 ++-- 7 files changed, 14 insertions(+), 8 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 3f4778bb..ddc7daa6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -7,6 +7,7 @@ lint: - tests/default.nf.test files_unchanged: - assets/nf-core-pixelator_logo_light.png + - .gitignore - .github/PULL_REQUEST_TEMPLATE.md multiqc_config: false nf_core_version: 4.0.2 diff --git a/main.nf b/main.nf index a7f26ad2..4a653cc9 100644 --- a/main.nf +++ b/main.nf @@ -40,7 +40,6 @@ workflow NFCORE_PIXELATOR { // PIXELATOR ( samplesheet, - params.outdir, ) } /* diff --git a/nextflow.config b/nextflow.config index 2a5ede6d..32f7bbb2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -105,7 +105,6 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false @@ -356,12 +355,21 @@ manifest { // Nextflow plugins plugins { id 'nf-schema@2.5.1' + id 'nf-slack@0.5.1' } validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } + +slack { + enabled = true + webhook { + url = System.getenv('HOOK_URL') + } +} + // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' includeConfig 'conf/modules.pna.config' diff --git a/nf-test.config b/nf-test.config index 0974c9a7..598e68d5 100644 --- a/nf-test.config +++ b/nf-test.config @@ -26,7 +26,7 @@ config { 'bin/*', 'conf/test.config', 'nextflow.config', - 'nextflow_schema.json' + 'nextflow_schema.json', 'nf-test.config', 'tests/.nftignore', 'tests/nextflow.config', diff --git a/subworkflows/local/pna/main.nf b/subworkflows/local/pna/main.nf index 90b37813..88f2042d 100644 --- a/subworkflows/local/pna/main.nf +++ b/subworkflows/local/pna/main.nf @@ -3,7 +3,6 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { softwareVersionsToYAML } from '../../nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index c7e54c3a..37e717e2 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -11,7 +11,6 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' @@ -29,7 +28,7 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - _monochrome_logs // boolean: Do not use coloured log outputs + monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index 8217a42f..8a56e923 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -142,10 +142,10 @@ workflow PIXELATOR { "${process}:\n${tool_versions.join('\n')}" } - def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${outdir}/pipeline_info", + storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_' + 'pixelator_software_' + 'versions.yml', sort: true, newLine: true From 266fe9e4ec9940d70af9146d4682c29ce8b6f330 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 10:12:53 +0200 Subject: [PATCH 22/90] Update snapshots --- subworkflows/local/pna/tests/main.nf.test | 1 - .../local/pna/tests/main.nf.test.snap | 11 +++++----- .../utils_nfcore_pixelator_pipeline/main.nf | 8 +++---- tests/default.nf.test | 2 +- tests/pna.nf.test | 4 ++-- tests/pna.nf.test.snap | 22 +++++++++---------- 6 files changed, 22 insertions(+), 26 deletions(-) diff --git a/subworkflows/local/pna/tests/main.nf.test b/subworkflows/local/pna/tests/main.nf.test index 3b2a5f68..05275ca3 100644 --- a/subworkflows/local/pna/tests/main.nf.test +++ b/subworkflows/local/pna/tests/main.nf.test @@ -42,7 +42,6 @@ nextflow_workflow { workflow.trace.succeeded().size(), // All stable path name, with a relative path stable_name, - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_mqc_versions.yml"), ).match() } ) } diff --git a/subworkflows/local/pna/tests/main.nf.test.snap b/subworkflows/local/pna/tests/main.nf.test.snap index 98207d42..702308f4 100644 --- a/subworkflows/local/pna/tests/main.nf.test.snap +++ b/subworkflows/local/pna/tests/main.nf.test.snap @@ -65,13 +65,12 @@ "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log", "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-graph.log", "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-layout.log" - ], - null + ] ], + "timestamp": "2026-05-06T10:58:35.023171035", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-12-04T12:48:00.492394412" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 37e717e2..44b47447 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -154,11 +154,9 @@ workflow PIPELINE_INITIALISATION { .combine(ch_panel_options) .combine(ch_design_options) .map { meta, panel_options, design_options -> - { - meta = validate_panel(meta, panel_options) - meta = validate_design(meta, design_options) - return meta - } + meta = validate_panel(meta, panel_options) + meta = validate_design(meta, design_options) + return meta } .join(ch_input) .map { meta, panel, reads -> diff --git a/tests/default.nf.test b/tests/default.nf.test index f2bedc30..e6cf7016 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), // All stable path name, with a relative path stable_path, // All files with stable contents diff --git a/tests/pna.nf.test b/tests/pna.nf.test index c1af17cb..5652b11e 100644 --- a/tests/pna.nf.test +++ b/tests/pna.nf.test @@ -33,7 +33,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), // All stable path name, with a relative path stable_name, ).match() } @@ -65,7 +65,7 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // All stable path name, with a relative path stable_name, - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), ).match() } ) } diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index a97d4339..3928c194 100644 --- a/tests/pna.nf.test.snap +++ b/tests/pna.nf.test.snap @@ -4,7 +4,7 @@ 20, [ "pipeline_info", - "pipeline_info/nf_core_pixelator_software_mqc_versions.yml", + "pipeline_info/nf_core_pixelator_software_versions.yml", "pipeline_info/samplesheet_pna.csv", "pixelator", "pixelator/PNA055_Sample07_filtered_S7.pxl", @@ -113,11 +113,11 @@ } } ], + "timestamp": "2026-05-06T14:20:09.408046793", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-19T08:54:43.966539669" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Params: all": { "content": [ @@ -159,7 +159,7 @@ }, [ "pipeline_info", - "pipeline_info/nf_core_pixelator_software_mqc_versions.yml", + "pipeline_info/nf_core_pixelator_software_versions.yml", "pipeline_info/samplesheet_pna.csv", "pixelator", "pixelator/PNA055_Sample07_filtered_S7.layout.pxl", @@ -249,10 +249,10 @@ "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-layout.log" ] ], + "timestamp": "2026-05-06T14:19:26.290381771", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-19T08:53:47.664150319" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } -} +} \ No newline at end of file From 59ca1c595f25b6c9567073a2c2f8e4bba1e7e3f4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 10:38:33 +0200 Subject: [PATCH 23/90] Contributing guidelines have been moved to docs/ --- .github/CONTRIBUTING.md | 125 ---------------------------------------- 1 file changed, 125 deletions(-) delete mode 100644 .github/CONTRIBUTING.md diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 9b4e68ba..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,125 +0,0 @@ -# `nf-core/pixelator`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/pixelator. - -We try to manage the required tasks for nf-core/pixelator using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/pixelator then the best place to ask is on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/pixelator, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/pixelator issues](https://github.com/nf-core/pixelator/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/pixelator repository](https://github.com/nf-core/pixelator) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Getting help - -For further information/help, please consult the [nf-core/pixelator documentation](https://nf-co.re/pixelator/usage) and don't hesitate to get in touch on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the `nf-core/pixelator` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/pixelator/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) From 160efb9886600530d85fbf8714e289ca6fa6b7a0 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 11:05:27 +0200 Subject: [PATCH 24/90] Remove default tests --- tests/default.nf.test | 33 --------------------------------- 1 file changed, 33 deletions(-) delete mode 100644 tests/default.nf.test diff --git a/tests/default.nf.test b/tests/default.nf.test deleted file mode 100644 index e6cf7016..00000000 --- a/tests/default.nf.test +++ /dev/null @@ -1,33 +0,0 @@ -nextflow_pipeline { - - name "Test pipeline" - script "../main.nf" - tag "pipeline" - - test("-profile test") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assert workflow.success - assertAll( - { assert snapshot( - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), - // All stable path name, with a relative path - stable_path, - // All files with stable contents - stable_content - ).match() } - ) - } - } -} From a13078b0585d16f1bfbe69254caec3467387501d Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 15:19:50 +0200 Subject: [PATCH 25/90] Fix linting errors and warnings --- .nf-core.yml | 1 + docs/CONTRIBUTING.md | 4 - modules/local/experiment_summary/meta.yml | 92 +++++++++++++ modules/local/pixelator/list_options/meta.yml | 57 ++++++++ .../single-cell-pna/amplicon/meta.yml | 93 +++++++++++++ .../single-cell-pna/analysis/meta.yml | 99 ++++++++++++++ .../single-cell-pna/collapse/meta.yml | 102 +++++++++++++++ .../single-cell-pna/combine_collapse/meta.yml | 96 ++++++++++++++ .../pixelator/single-cell-pna/demux/meta.yml | 122 ++++++++++++++++++ .../single-cell-pna/denoise/meta.yml | 99 ++++++++++++++ .../pixelator/single-cell-pna/graph/meta.yml | 106 +++++++++++++++ .../pixelator/single-cell-pna/layout/meta.yml | 99 ++++++++++++++ .../local/pna/generate_reports/meta.yml | 83 ++++++++++++ subworkflows/local/pna/meta.yml | 52 ++++++++ .../utils_nfcore_pixelator_pipeline/main.nf | 6 +- .../utils_nfcore_pixelator_pipeline/meta.yml | 76 +++++++++++ 16 files changed, 1180 insertions(+), 7 deletions(-) create mode 100644 modules/local/experiment_summary/meta.yml create mode 100644 modules/local/pixelator/list_options/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/amplicon/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/analysis/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/collapse/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/demux/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/denoise/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/graph/meta.yml create mode 100644 modules/local/pixelator/single-cell-pna/layout/meta.yml create mode 100644 subworkflows/local/pna/generate_reports/meta.yml create mode 100644 subworkflows/local/pna/meta.yml create mode 100644 subworkflows/local/utils_nfcore_pixelator_pipeline/meta.yml diff --git a/.nf-core.yml b/.nf-core.yml index ddc7daa6..b6cb2636 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,6 +9,7 @@ lint: - assets/nf-core-pixelator_logo_light.png - .gitignore - .github/PULL_REQUEST_TEMPLATE.md + - LICENSE multiqc_config: false nf_core_version: 4.0.2 repository_type: pipeline diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index da58ce71..e8aea4f3 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -176,7 +176,3 @@ nf-core pipelines bump-version --nextflow . #### Images and figures guidelines If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics). - -## Pipeline specific contribution guidelines - - diff --git a/modules/local/experiment_summary/meta.yml b/modules/local/experiment_summary/meta.yml new file mode 100644 index 00000000..c6ed379d --- /dev/null +++ b/modules/local/experiment_summary/meta.yml @@ -0,0 +1,92 @@ +name: experiment_summary +description: Generate an HTML experiment summary report from pipeline outputs. +keywords: + - report + - quarto + - summary + - experiment +tools: + - experiment-summary: + description: Pixelator experiment summary report generation with pixelatorES. + homepage: https://pixelgen.com/ + documentation: https://github.com/PixelgenTechnologies/pixelatorES + licence: ["MIT"] + identifier: "" +input: + - - samplesheet_path: + type: file + description: Sample sheet used for the experiment. + pattern: "*.{csv,tsv,txt}" + ontologies: [] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - amplicon_data: + type: file + description: Inputs staged under results/amplicon. + ontologies: [] + - demux_data: + type: file + description: Inputs staged under results/demux. + ontologies: [] + - collapse_data: + type: file + description: Inputs staged under results/collapse. + ontologies: [] + - graph_data: + type: file + description: Inputs staged under results/graph. + ontologies: [] + - denoise_data: + type: file + description: Inputs staged under results/denoise. + ontologies: [] + - analysis_data: + type: file + description: Inputs staged under results/analysis. + ontologies: [] + - layout_data: + type: file + description: Inputs staged under results/layout. + ontologies: [] +output: + html: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*experiment-summary.html": + type: file + description: Generated experiment summary HTML report. + pattern: "*experiment-summary.html" + ontologies: [] + versions_experiment_summary: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - experiment-summary: + type: string + description: The tool name. + - Rscript -e 'cat(as.character(packageVersion("pixelatorES")), "\n")': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - experiment-summary: + type: string + description: The tool name. + - Rscript -e 'cat(as.character(packageVersion("pixelatorES")), "\n")': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/list_options/meta.yml b/modules/local/pixelator/list_options/meta.yml new file mode 100644 index 00000000..5889867d --- /dev/null +++ b/modules/local/pixelator/list_options/meta.yml @@ -0,0 +1,57 @@ +name: pixelator_list_options +description: List available Pixelator single-cell-pna design and panel options. +keywords: + - pixelator + - single-cell-pna + - list + - options +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: [] +output: + designs: + - - design_options.txt: + type: file + description: Text file containing available design options. + pattern: "design_options.txt" + ontologies: [] + panels: + - - panel_options.txt: + type: file + description: Text file containing available panel options. + pattern: "panel_options.txt" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/amplicon/meta.yml b/modules/local/pixelator/single-cell-pna/amplicon/meta.yml new file mode 100644 index 00000000..ab24d3bc --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/amplicon/meta.yml @@ -0,0 +1,93 @@ +name: pixelator_pna_amplicon +description: Run `pixelator single-cell-pna amplicon` on input FASTQ files. +keywords: + - pixelator + - single-cell-pna + - amplicon + - fastq +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - reads: + type: file + description: Input FASTQ files. + pattern: "*.{fq,fastq,fq.gz,fastq.gz,fq.zst,fastq.zst}" + ontologies: + - http://edamontology.org/format_2545 +output: + amplicon: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.amplicon.{fq,fastq}.zst": + type: file + description: Amplicon FASTQ output. + pattern: "*.{fq,fastq}.zst" + ontologies: + - http://edamontology.org/format_2545 + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-amplicon.log": + type: file + description: Pixelator amplicon command log. + pattern: "*pixelator-amplicon.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/analysis/meta.yml b/modules/local/pixelator/single-cell-pna/analysis/meta.yml new file mode 100644 index 00000000..7ea66469 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/analysis/meta.yml @@ -0,0 +1,99 @@ +name: pixelator_pna_analysis +description: Run `pixelator single-cell-pna analysis` on pixel data. +keywords: + - pixelator + - single-cell-pna + - analysis + - pxl +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - data: + type: file + description: Input file for the analysis subcommand. + ontologies: [] +output: + pixelfile: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.pxl": + type: file + description: Pixelator PXL output file. + pattern: "*.pxl" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + all_results: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*": + type: directory + description: All files generated in the analysis output directory. + pattern: "*" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-analysis.log": + type: file + description: Pixelator analysis command log. + pattern: "*pixelator-analysis.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/collapse/meta.yml b/modules/local/pixelator/single-cell-pna/collapse/meta.yml new file mode 100644 index 00000000..808c7d54 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/collapse/meta.yml @@ -0,0 +1,102 @@ +name: pixelator_pna_collapse +description: Run `pixelator single-cell-pna collapse` to collapse reads into molecule-level parquet outputs. +keywords: + - pixelator + - single-cell-pna + - collapse + - parquet +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', design:'pna-2' ] + - reads: + type: file + description: Input FASTQ files. + pattern: "*.{fq,fastq,fq.gz,fastq.gz,fq.zst,fastq.zst}" + ontologies: + - http://edamontology.org/format_2545 + - panel_file: + type: file + description: Optional panel definition file. + ontologies: [] + - panel: + type: string + description: Optional panel name. + - design: + type: string + description: Assay design identifier. +output: + collapsed: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.parquet": + type: file + description: Collapsed molecule-level parquet output(s). + pattern: "*.parquet" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-collapse.log": + type: file + description: Pixelator collapse command log. + pattern: "*pixelator-collapse.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml b/modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml new file mode 100644 index 00000000..0da34349 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml @@ -0,0 +1,96 @@ +name: pixelator_pna_combine_collapse +description: Run `pixelator single-cell-pna combine-collapse` to merge multiple collapse outputs. +keywords: + - pixelator + - single-cell-pna + - combine-collapse + - parquet +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - parquet_files: + type: file + description: Parquet files produced by collapse. + pattern: "*.parquet" + ontologies: [] + - json_report_files: + type: file + description: JSON reports associated with collapse parquet files. + pattern: "*.report.json" + ontologies: [] +output: + parquet: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.parquet": + type: file + description: Combined collapse parquet output. + pattern: "*.parquet" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-combine-collapse.log": + type: file + description: Pixelator combine-collapse command log. + pattern: "*pixelator-combine-collapse.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/demux/meta.yml b/modules/local/pixelator/single-cell-pna/demux/meta.yml new file mode 100644 index 00000000..07de6b84 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/demux/meta.yml @@ -0,0 +1,122 @@ +name: pixelator_pna_demux +description: Run `pixelator single-cell-pna demux` to split reads and generate demultiplexed outputs. +keywords: + - pixelator + - single-cell-pna + - demux + - parquet +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', design:'pna-2' ] + - reads: + type: file + description: Input FASTQ files. + pattern: "*.{fq,fastq,fq.gz,fastq.gz,fq.zst,fastq.zst}" + ontologies: + - http://edamontology.org/format_2545 + - panel_file: + type: file + description: Optional panel definition file. + ontologies: [] + - panel: + type: string + description: Optional panel name. + - design: + type: string + description: Assay design identifier. +output: + demuxed: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.parquet": + type: file + description: Demultiplexed parquet output(s). + pattern: "*.parquet" + ontologies: [] + passed: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*demux.passed*.{fq,fastq}.zst": + type: file + description: Reads that passed demultiplexing. + pattern: "*demux.passed*.{fq,fastq}.zst" + ontologies: + - http://edamontology.org/format_2545 + failed: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*demux.failed.{fq,fastq}.zst": + type: file + description: Reads that failed demultiplexing. + pattern: "*demux.failed.{fq,fastq}.zst" + ontologies: + - http://edamontology.org/format_2545 + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-demux.log": + type: file + description: Pixelator demux command log. + pattern: "*pixelator-demux.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/denoise/meta.yml b/modules/local/pixelator/single-cell-pna/denoise/meta.yml new file mode 100644 index 00000000..783497f4 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/denoise/meta.yml @@ -0,0 +1,99 @@ +name: pixelator_pna_denoise +description: Run `pixelator single-cell-pna denoise` on graph output data. +keywords: + - pixelator + - single-cell-pna + - denoise + - pxl +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - data: + type: file + description: Input file for the denoise subcommand. + ontologies: [] +output: + pixelfile: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.pxl": + type: file + description: Pixelator PXL output file. + pattern: "*.pxl" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + all_results: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*": + type: directory + description: All files generated in the denoise output directory. + pattern: "*" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-denoise.log": + type: file + description: Pixelator denoise command log. + pattern: "*pixelator-denoise.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/graph/meta.yml b/modules/local/pixelator/single-cell-pna/graph/meta.yml new file mode 100644 index 00000000..5b78eae0 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/graph/meta.yml @@ -0,0 +1,106 @@ +name: pixelator_pna_graph +description: Run `pixelator single-cell-pna graph` to build graph-level pixel files. +keywords: + - pixelator + - single-cell-pna + - graph + - pxl +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - edge_list: + type: file + description: Input edge list parquet file. + ontologies: [] + - panel_file: + type: file + description: Optional panel definition file. + ontologies: [] + - panel: + type: string + description: Optional panel name. +output: + all_results: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*": + type: directory + description: All files generated in the graph output directory. + pattern: "*" + ontologies: [] + pixelfile: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.pxl": + type: file + description: Pixelator PXL output file. + pattern: "*.pxl" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-graph.log": + type: file + description: Pixelator graph command log. + pattern: "*pixelator-graph.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/modules/local/pixelator/single-cell-pna/layout/meta.yml b/modules/local/pixelator/single-cell-pna/layout/meta.yml new file mode 100644 index 00000000..93cec7b9 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/layout/meta.yml @@ -0,0 +1,99 @@ +name: pixelator_pna_layout +description: Run `pixelator single-cell-pna layout` to compute layout outputs from pixel data. +keywords: + - pixelator + - single-cell-pna + - layout + - pxl +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - data: + type: file + description: Input file for the layout subcommand. + ontologies: [] +output: + pixelfile: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.pxl": + type: file + description: Pixelator PXL output file. + pattern: "*.pxl" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.report.json": + type: file + description: Run report in JSON format. + pattern: "*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "*.meta.json" + ontologies: [] + all_results: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*": + type: directory + description: All files generated in the layout output directory. + pattern: "*" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-layout.log": + type: file + description: Pixelator layout command log. + pattern: "*pixelator-layout.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/subworkflows/local/pna/generate_reports/meta.yml b/subworkflows/local/pna/generate_reports/meta.yml new file mode 100644 index 00000000..7fac5b6c --- /dev/null +++ b/subworkflows/local/pna/generate_reports/meta.yml @@ -0,0 +1,83 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: pna_generate_reports +description: Aggregate Pixelator stage outputs and generate an experiment summary report. +keywords: + - pixelator + - pna + - report + - summary +components: + - experiment/summary +input: + - samplesheet: + type: file + description: | + Input channel containing the sample sheet path. + Structure: [ path(samplesheet) ] + pattern: "*.{csv,tsv,txt}" + - panel_files: + type: file + description: | + Input channel containing panel files per sample. + Structure: [ val(meta), path(panel_file) ] + pattern: "*" + - amplicon_data: + type: file + description: | + Input channel with amplicon report and metadata files per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*.{json,meta.json,report.json}" + - demux_data: + type: file + description: | + Input channel with demux report and metadata files per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*.{json,meta.json,report.json}" + - collapse_data: + type: file + description: | + Input channel with collapse report and metadata files per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*.{json,meta.json,report.json}" + - graph_data: + type: file + description: | + Input channel with graph outputs per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*" + - denoise_data: + type: file + description: | + Input channel with denoise outputs per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*" + - analysis_data: + type: file + description: | + Input channel with analysis outputs per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*" + - layout_data: + type: file + description: | + Input channel with layout report and metadata files per sample. + Structure: [ val(meta), [ path(file), ... ] ] + pattern: "*.{json,meta.json,report.json}" + - skip_experiment_summary: + type: boolean + description: Boolean flag controlling whether experiment summary generation is skipped. +output: + - experiment_summary: + type: file + description: | + Channel containing experiment summary HTML files when enabled, or empty placeholders when skipped. + Structure: [ val(meta), path("*.html") ] + pattern: "*.html" +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/subworkflows/local/pna/meta.yml b/subworkflows/local/pna/meta.yml new file mode 100644 index 00000000..6d581234 --- /dev/null +++ b/subworkflows/local/pna/meta.yml @@ -0,0 +1,52 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: pna +description: Run the Pixelator single-cell PNA workflow from FASTQ input through graph and analysis outputs. +keywords: + - pixelator + - pna + - single-cell + - fastq +components: + - pixelator/pna/amplicon + - pixelator/pna/demux + - pixelator/pna/collapse + - pixelator/pna/combine/collapse + - pixelator/pna/graph + - pixelator/pna/denoise + - pixelator/pna/analysis + - pixelator/pna/layout + - pna_generate_reports +input: + - fastq: + type: file + description: | + Input channel containing sample metadata and one or more FASTQ files. + Structure: [ val(meta), path(reads) ] + pattern: "*.{fq,fastq,fq.gz,fastq.gz,fq.zst,fastq.zst}" + - panel_files: + type: file + description: | + Input channel containing sample metadata and optional panel definition files. + Structure: [ val(meta), path(panel_file) ] + pattern: "*" +output: + - graph: + type: file + description: | + Channel containing graph-stage pixel files. + Structure: [ val(meta), path("*.pxl") ] + pattern: "*.pxl" + - analysis: + type: file + description: | + Channel containing analysis-stage pixel files. + Structure: [ val(meta), path("*.pxl") ] + pattern: "*.pxl" +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 44b47447..63de15cf 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -247,7 +247,7 @@ def getGenomeAttribute(attribute) { // Generate methods description for MultiQC // def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. + // nf-core: Optionally add in-text citation tools to this list. // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ @@ -259,7 +259,7 @@ def toolCitationText() { } def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. + // nf-core: Optionally add bibliographic entries to this list. // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ @@ -295,7 +295,7 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["tool_citations"] = "" meta["tool_bibliography"] = "" - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") // meta["tool_bibliography"] = toolBibliographyText() diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/meta.yml b/subworkflows/local/utils_nfcore_pixelator_pipeline/meta.yml new file mode 100644 index 00000000..6dadbe56 --- /dev/null +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/meta.yml @@ -0,0 +1,76 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: pipeline_initialisation +description: Provide nf-core/pixelator-specific pipeline utility subworkflows for initialization and completion hooks. +keywords: + - nf-core + - pixelator + - pipeline + - utilities +components: + - utils_nfschema_plugin + - utils_nfcore_pipeline + - utils_nextflow_pipeline + - pixelator/list/options + - completionemail + - completionsummary +input: + - version: + type: boolean + description: Boolean flag to print version information and exit. + - validate_params: + type: boolean + description: Boolean flag to validate runtime parameters against schema. + - monochrome_logs: + type: boolean + description: Boolean flag to disable ANSI colors in logging output. + - nextflow_cli_args: + type: list + description: Positional Nextflow CLI arguments. + - outdir: + type: string + description: Output directory where results are written. + - input: + type: string + description: Path to the input samplesheet. + - input_basedir: + type: string + description: Optional base path used for resolving relative input paths. + - help: + type: boolean + description: Boolean flag to display help and exit. + - help_full: + type: boolean + description: Boolean flag to display extended help and exit. + - show_hidden: + type: boolean + description: Boolean flag to include hidden parameters in help. + - email: + type: string + description: Email address for completion notifications. + - email_on_fail: + type: string + description: Email address for notifications on workflow failure. + - plaintext_email: + type: boolean + description: Boolean flag to send plain-text completion emails. +output: + - samplesheet: + type: file + description: | + Channel containing validated samplesheet entries and resolved input paths. + Structure: [ val(meta), path(panel_file), path(reads) ] + pattern: "*" + - versions: + type: file + description: | + Channel intended to collect version information generated in initialization. + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" From 085c6f78a3d000afcefd598dc650f769e6c09424 Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Tue, 12 May 2026 11:04:26 +0200 Subject: [PATCH 26/90] Setup input specific resource configs --- CHANGELOG.md | 1 + README.md | 2 +- conf/cells_1k.config | 43 +++++++++++++++++++++++++++++++++++++++++++ conf/cells_8k.config | 43 +++++++++++++++++++++++++++++++++++++++++++ docs/usage.md | 12 +++++++++--- nextflow.config | 8 ++++++++ 6 files changed, 105 insertions(+), 4 deletions(-) create mode 100644 conf/cells_1k.config create mode 100644 conf/cells_8k.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 3de29736..88560861 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) - Updated pixelatorES to 0.6.0 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197) +- Add `cells_1k` and `cells_8k` Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg [#202](https://github.com/nf-core/pixelator/pull/202) ### Software dependencies diff --git a/README.md b/README.md index ec345b64..38c3715f 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Now, you can run the pipeline using: ```bash nextflow run nf-core/pixelator \ - -profile \ + -profile , \ --input samplesheet.csv \ --outdir ``` diff --git a/conf/cells_1k.config b/conf/cells_1k.config new file mode 100644 index 00000000..5253119b --- /dev/null +++ b/conf/cells_1k.config @@ -0,0 +1,43 @@ +process { + // All processes not defined here will rely on process labels and base.config. + + withName: PIXELATOR_PNA_AMPLICON { + cpus = { 32 * task.attempt } + memory = { 32.GB * task.attempt } + time = { 4.h * task.attempt } + } + + withName: PIXELATOR_PNA_DEMUX { + cpus = { 16 * task.attempt } + memory = { 64.GB * task.attempt } + time = { 4.h * task.attempt } + } + + withName: PIXELATOR_PNA_COLLAPSE { + cpus = { 8 * task.attempt } + memory = { 64.GB * task.attempt } + time = { 8.h * task.attempt } + maxRetries = 4 + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } + } + + withName: PIXELATOR_PNA_COMBINE_COLLAPSE { + cpus = { 16 * task.attempt } + memory = { 128.GB * task.attempt } + time = { 4.h * task.attempt } + maxRetries = 4 + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } + } + + withName: PIXELATOR_PNA_GRAPH { + cpus = { 12 * task.attempt } + memory = { 512.GB * task.attempt } + time = { 10.h * task.attempt } + } + + withName: EXPERIMENT_SUMMARY { + cpus = { 16 * task.attempt } + memory = { 64.GB * task.attempt } + time = { 12.h * task.attempt } + } +} diff --git a/conf/cells_8k.config b/conf/cells_8k.config new file mode 100644 index 00000000..4a592cf5 --- /dev/null +++ b/conf/cells_8k.config @@ -0,0 +1,43 @@ +process { + // Keep process sizing overrides here for larger (8k cell) runs. + + withName: PIXELATOR_PNA_AMPLICON { + cpus = { 32 * task.attempt } + memory = { 32.GB * task.attempt } + time = { 40.h * task.attempt } + } + + withName: PIXELATOR_PNA_DEMUX { + cpus = { 16 * task.attempt } + memory = { 128.GB * task.attempt } + time = { 12.h * task.attempt } + } + + withName: PIXELATOR_PNA_COLLAPSE { + cpus = { 8 * task.attempt } + memory = { 256.GB * task.attempt } + time = { 8.h * task.attempt } + maxRetries = 4 + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } + } + + withName: PIXELATOR_PNA_COMBINE_COLLAPSE { + cpus = { 8 * task.attempt } + memory = { 512.GB * task.attempt } + time = { 6.h * task.attempt } + maxRetries = 4 + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } + } + + withName: PIXELATOR_PNA_GRAPH { + cpus = { 12 * task.attempt } + memory = { 512.GB * task.attempt } + time = { 20.h * task.attempt } + } + + withName: EXPERIMENT_SUMMARY { + cpus = { 16 * task.attempt } + memory = { 64.GB * task.attempt } + time = { 12.h * task.attempt } + } +} diff --git a/docs/usage.md b/docs/usage.md index 6e3fef34..f2b1829b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -139,10 +139,12 @@ pixelator single-cell-pna --list-panels The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results -profile docker +nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results -profile docker,cells_8k ``` -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. +This will launch the pipeline with the `docker` configuration profile, and resource configurations +for 8000 cells. If you have samples with 1000 cells as input, pick the `cells_1k` profile instead. +See below for more information about profiles. Note that the pipeline will create the following files in your working directory: @@ -163,7 +165,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < The above pipeline run specified with a params file in yaml format: ```bash -nextflow run nf-core/pixelator -profile docker -params-file params.yaml +nextflow run nf-core/pixelator -profile docker,cells_8k -params-file params.yaml ``` with: @@ -242,6 +244,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). +- `cells_8k` + - A configuration profile for 8000 cells. +- `cells_1k` + - A configuration profile for 1000 cells. :::warning Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. diff --git a/nextflow.config b/nextflow.config index e333874a..fb9e4be2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,6 +254,14 @@ profiles { test_full { includeConfig 'conf/test_full.config' } + + cells_1k { + includeConfig 'conf/cells_1k.config' + } + + cells_8k { + includeConfig 'conf/cells_8k.config' + } } // Load nf-core custom profiles from different institutions includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" From 8ce5ae7a568e607de58fa4c0effe9f5abf33ba8d Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 22 Apr 2026 08:53:41 +0200 Subject: [PATCH 27/90] Update pixelator to 0.26.0 --- CHANGELOG.md | 15 ++++++++ conf/modules.pna.config | 4 +-- modules/local/pixelator/list_options/main.nf | 4 +-- .../single-cell-pna/amplicon/main.nf | 4 +-- .../amplicon/tests/main.nf.test.snap | 6 ++-- .../single-cell-pna/analysis/main.nf | 4 +-- .../analysis/tests/main.nf.test.snap | 6 ++-- .../single-cell-pna/collapse/main.nf | 4 +-- .../collapse/tests/main.nf.test.snap | 6 ++-- .../single-cell-pna/combine_collapse/main.nf | 4 +-- .../combine_collapse/tests/main.nf.test.snap | 6 ++-- .../pixelator/single-cell-pna/demux/main.nf | 4 +-- .../demux/tests/main.nf.test.snap | 8 ++--- .../pixelator/single-cell-pna/denoise/main.nf | 4 +-- .../denoise/tests/main.nf.test.snap | 6 ++-- .../pixelator/single-cell-pna/graph/main.nf | 4 +-- .../graph/tests/main.nf.test.snap | 6 ++-- .../pixelator/single-cell-pna/layout/main.nf | 4 +-- .../layout/tests/main.nf.test.snap | 6 ++-- nextflow.config | 8 ++--- nextflow_schema.json | 27 +++++--------- tests/pna.nf.test.snap | 36 +++++++++---------- 22 files changed, 88 insertions(+), 88 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 88560861..5a01e2be 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ------------- | ----------- | ----------- | | `pixelatorES` | 0.6.0 | 0.8.6 | +| `pixelatorES` | 0.23.0 | 0.26.0 | + +### Parameters + +| Old parameter | New parameter | +| ---------------------------------------- | -------------------------------- | +| `--leiden-iterations` | | +| `--min-component-size-in-refinement` | | +| `--min-component-size-to-prune` | | +| | `--edge_cycle-verification` | + +> [!NOTE] +> Parameter has been **updated** if both old and new parameter information is present. +> Parameter has been **added** if just the new parameter information is present. +> Parameter has been **removed** if new parameter information isn't present. ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 diff --git a/conf/modules.pna.config b/conf/modules.pna.config index 4076e065..1c9da75a 100644 --- a/conf/modules.pna.config +++ b/conf/modules.pna.config @@ -122,17 +122,15 @@ process { ext.args = { [ params.pna_graph_multiplet_recovery ? "--multiplet-recovery" : '', - params.pna_graph_leiden_iterations ? "--leiden-iterations ${params.pna_graph_leiden_iterations}" : '', + params.pna_graph_edge_cycle_verification ? "--edge-cycle-verification" : '', params.pna_graph_initial_stage_leiden_resolution ? "--initial-stage-leiden-resolution ${params.pna_graph_initial_stage_leiden_resolution}" : '', params.pna_graph_refinement_stage_leiden_resolution ? "--refinement-stage-leiden-resolution ${params.pna_graph_refinement_stage_leiden_resolution}" : '', params.pna_graph_min_count ? "--min-count ${params.pna_graph_min_count}" : '', - params.pna_graph_min_component_size_in_refinement ? "--min-component-size-in-refinement ${params.pna_graph_min_component_size_in_refinement}" : '', params.pna_graph_max_refinement_recursion_depth ? "--max-refinement-recursion-depth ${params.pna_graph_max_refinement_recursion_depth}" : '', params.pna_graph_initial_stage_max_edges_to_remove ? "--initial-stage-max-edges-to-remove ${params.pna_graph_initial_stage_max_edges_to_remove}" : '', params.pna_graph_refinement_stage_max_edges_to_remove ? "--refinement-stage-max-edges-to-remove ${params.pna_graph_refinement_stage_max_edges_to_remove}" : '', params.pna_graph_initial_stage_max_edges_to_remove_relative ? "--initial-stage-max-edges-to-remove-relative ${params.pna_graph_initial_stage_max_edges_to_remove_relative}" : '', params.pna_graph_refinement_stage_max_edges_to_remove_relative ? "--refinement-stage-max-edges-to-remove-relative ${params.pna_graph_refinement_stage_max_edges_to_remove_relative}" : '', - params.pna_graph_graph_min_component_size_to_prune ? "--min-component-size-to-prune ${params.pna_graph_graph_min_component_size_to_prune}" : '', params.pna_graph_component_size_min_threshold ? "--component-size-min-threshold ${params.pna_graph_component_size_min_threshold}" : '', ].join(' ').trim() } diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf index dd24023f..9ed92e48 100644 --- a/modules/local/pixelator/list_options/main.nf +++ b/modules/local/pixelator/list_options/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_LIST_OPTIONS { // TODO: Add conda back // conda "${moduleDir}/environment.yml" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" output: path "design_options.txt", emit: designs diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/single-cell-pna/amplicon/main.nf index e1ec72fd..378e661a 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/main.nf +++ b/modules/local/pixelator/single-cell-pna/amplicon/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_PNA_AMPLICON { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(reads, arity: '1..*') diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap index 5f396d08..8022e139 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap @@ -50,7 +50,7 @@ [ "PIXELATOR_PNA_AMPLICON", "pixelator", - "0.23.0" + "0.26.0" ] ], "amplicon": [ @@ -101,7 +101,7 @@ [ "PIXELATOR_PNA_AMPLICON", "pixelator", - "0.23.0" + "0.26.0" ] ] } @@ -128,7 +128,7 @@ [ "PIXELATOR_PNA_AMPLICON", "pixelator", - "0.23.0" + "0.26.0" ] ] ], diff --git a/modules/local/pixelator/single-cell-pna/analysis/main.nf b/modules/local/pixelator/single-cell-pna/analysis/main.nf index 78cb0533..90fe224e 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/main.nf +++ b/modules/local/pixelator/single-cell-pna/analysis/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_PNA_ANALYSIS { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap index f497c737..1836f23a 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "PIXELATOR_PNA_ANALYSIS", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -91,7 +91,7 @@ [ "PIXELATOR_PNA_ANALYSIS", "pixelator", - "0.23.0" + "0.26.0" ] ], "all_results": [ @@ -157,7 +157,7 @@ [ "PIXELATOR_PNA_ANALYSIS", "pixelator", - "0.23.0" + "0.26.0" ] ] } diff --git a/modules/local/pixelator/single-cell-pna/collapse/main.nf b/modules/local/pixelator/single-cell-pna/collapse/main.nf index 4251de7c..6fc43487 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/collapse/main.nf @@ -7,8 +7,8 @@ process PIXELATOR_PNA_COLLAPSE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap index c351c53b..41433356 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "PIXELATOR_PNA_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -80,7 +80,7 @@ [ "PIXELATOR_PNA_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ], "collapsed": [ @@ -135,7 +135,7 @@ [ "PIXELATOR_PNA_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ] } diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf index 3ecb4c19..c16bf0d0 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_PNA_COMBINE_COLLAPSE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(parquet_files, stageAs: "parquet/*"), path(json_report_files, stageAs: "reports/*") diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap index 79c3e70e..2d7047ad 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "PIXELATOR_PNA_COMBINE_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -76,7 +76,7 @@ [ "PIXELATOR_PNA_COMBINE_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ], "log": [ @@ -127,7 +127,7 @@ [ "PIXELATOR_PNA_COMBINE_COLLAPSE", "pixelator", - "0.23.0" + "0.26.0" ] ] } diff --git a/modules/local/pixelator/single-cell-pna/demux/main.nf b/modules/local/pixelator/single-cell-pna/demux/main.nf index e2490760..b8ca5407 100644 --- a/modules/local/pixelator/single-cell-pna/demux/main.nf +++ b/modules/local/pixelator/single-cell-pna/demux/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_PNA_DEMUX { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap index 325861bc..3b667dcc 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "PIXELATOR_PNA_DEMUX", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -101,7 +101,7 @@ [ "PIXELATOR_PNA_DEMUX", "pixelator", - "0.23.0" + "0.26.0" ] ], "demuxed": [ @@ -177,7 +177,7 @@ [ "PIXELATOR_PNA_DEMUX", "pixelator", - "0.23.0" + "0.26.0" ] ] } @@ -204,7 +204,7 @@ [ "PIXELATOR_PNA_DEMUX", "pixelator", - "0.23.0" + "0.26.0" ] ] ], diff --git a/modules/local/pixelator/single-cell-pna/denoise/main.nf b/modules/local/pixelator/single-cell-pna/denoise/main.nf index 02cb20ee..337df233 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/main.nf +++ b/modules/local/pixelator/single-cell-pna/denoise/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_PNA_DENOISE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap index 4044f38a..d6ed52c1 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "PIXELATOR_PNA_DENOISE", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -91,7 +91,7 @@ [ "PIXELATOR_PNA_DENOISE", "pixelator", - "0.23.0" + "0.26.0" ] ], "all_results": [ @@ -157,7 +157,7 @@ [ "PIXELATOR_PNA_DENOISE", "pixelator", - "0.23.0" + "0.26.0" ] ] } diff --git a/modules/local/pixelator/single-cell-pna/graph/main.nf b/modules/local/pixelator/single-cell-pna/graph/main.nf index 372a5cf4..fb49f8c8 100644 --- a/modules/local/pixelator/single-cell-pna/graph/main.nf +++ b/modules/local/pixelator/single-cell-pna/graph/main.nf @@ -4,8 +4,8 @@ process PIXELATOR_PNA_GRAPH { label 'process_long' container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(edge_list), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap index 56632406..50b27333 100644 --- a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap @@ -65,7 +65,7 @@ [ "PIXELATOR_PNA_GRAPH", "pixelator", - "0.23.0" + "0.26.0" ] ], "all_results": [ @@ -131,7 +131,7 @@ [ "PIXELATOR_PNA_GRAPH", "pixelator", - "0.23.0" + "0.26.0" ] ] } @@ -158,7 +158,7 @@ [ "PIXELATOR_PNA_GRAPH", "pixelator", - "0.23.0" + "0.26.0" ] ] ], diff --git a/modules/local/pixelator/single-cell-pna/layout/main.nf b/modules/local/pixelator/single-cell-pna/layout/main.nf index 0b85fbff..3b565a50 100644 --- a/modules/local/pixelator/single-cell-pna/layout/main.nf +++ b/modules/local/pixelator/single-cell-pna/layout/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_PNA_LAYOUT { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.23.0' - : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap index 96a3b9eb..2081e913 100644 --- a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap @@ -16,7 +16,7 @@ [ "PIXELATOR_PNA_LAYOUT", "pixelator", - "0.23.0" + "0.26.0" ] ] ], @@ -92,7 +92,7 @@ [ "PIXELATOR_PNA_LAYOUT", "pixelator", - "0.23.0" + "0.26.0" ] ], "all_results": [ @@ -158,7 +158,7 @@ [ "PIXELATOR_PNA_LAYOUT", "pixelator", - "0.23.0" + "0.26.0" ] ] } diff --git a/nextflow.config b/nextflow.config index 2b831f67..04e6f0ef 100644 --- a/nextflow.config +++ b/nextflow.config @@ -57,17 +57,15 @@ params { // PNA graph pna_graph_multiplet_recovery = true - pna_graph_leiden_iterations = 1 pna_graph_initial_stage_leiden_resolution = 1.0 pna_graph_refinement_stage_leiden_resolution = 0.01 pna_graph_min_count = 1 - pna_graph_min_component_size_in_refinement = 1000 - pna_graph_max_refinement_recursion_depth = 5 + pna_graph_max_refinement_recursion_depth = 3 + pna_graph_edge_cycle_verification = true pna_graph_initial_stage_max_edges_to_remove = null - pna_graph_refinement_stage_max_edges_to_remove = 4 + pna_graph_refinement_stage_max_edges_to_remove = 10 pna_graph_initial_stage_max_edges_to_remove_relative = null pna_graph_refinement_stage_max_edges_to_remove_relative = null - pna_graph_graph_min_component_size_to_prune = 100 pna_graph_component_size_min_threshold = 8000 // PNA denoise diff --git a/nextflow_schema.json b/nextflow_schema.json index a093a684..0bf50ca5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -205,12 +205,6 @@ "type": "boolean", "default": true }, - "pna_graph_leiden_iterations": { - "type": "integer", - "default": 1, - "description": "Number of iterations for the leiden algorithm.", - "help": "High values will decrease the variance of the results but increase the runtime" - }, "pna_graph_initial_stage_leiden_resolution": { "default": 1, "minimum": 0, @@ -225,6 +219,12 @@ "description": "The resolution parameter for the leiden algorithm at the refinement stage.", "help": "This should typically be set lower than the initial stage resolution." }, + "pna_graph_edge_cycle_verification": { + "type": "boolean", + "default": true, + "description": "Activate edge cycle verification to remove edges from well connected regions that are not part of cycles in the graph.", + "help": "This option can help improve the quality of the graph by removing potentially false edges." + }, "pna_graph_min_count": { "default": 1, "maximum": 50, @@ -232,21 +232,16 @@ "type": "number", "description": "Discard edges with a read count below given value. Set to 1 to disable filtering." }, - "pna_graph_min_component_size_in_refinement": { - "type": "integer", - "default": 1000, - "minimum": 1, - "description": "The minimum component size to consider for refinement" - }, "pna_graph_max_refinement_recursion_depth": { "type": "integer", - "default": 5, + "default": 3, "minimum": 1, "maximum": 100, "description": "The maximum recursion depth for the refinement algorithm. Set to 1 to disable refinement." }, "pna_graph_initial_stage_max_edges_to_remove": { "type": "integer", + "default": 10, "minimum": 1, "description": "The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery." }, @@ -266,12 +261,6 @@ "minimum": 0, "description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery." }, - "pna_graph_graph_min_component_size_to_prune": { - "type": "integer", - "minimum": 1, - "default": 100, - "description": "The minimum number of nodes in an potential new components in order for it to be pruned." - }, "pna_graph_component_size_min_threshold": { "type": "integer", "minimum": 1, diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index 3928c194..21909ad7 100644 --- a/tests/pna.nf.test.snap +++ b/tests/pna.nf.test.snap @@ -82,31 +82,31 @@ "experiment-summary": "0.8.6" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_AMPLICON": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_ANALYSIS": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_COLLAPSE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_COMBINE_COLLAPSE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_DEMUX": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_DENOISE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_GRAPH": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_LAYOUT": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "Workflow": { "nf-core/pixelator": "v3.1.0dev" @@ -127,31 +127,31 @@ "experiment-summary": "0.8.6" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_AMPLICON": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_ANALYSIS": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_COLLAPSE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_COMBINE_COLLAPSE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_DEMUX": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_DENOISE": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_GRAPH": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "PIXELATOR_PNA_LAYOUT": { - "pixelator": "0.23.0" + "pixelator": "0.26.0" }, "Workflow": { "nf-core/pixelator": "v3.1.0dev" From 44eaa32d41fdeab173d25393a004d9852435f2bc Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 22 Apr 2026 08:50:24 +0200 Subject: [PATCH 28/90] Add pna v2 subworkflow --- .../single-cell-pna/sample_calling/main.nf | 72 +++++ .../sample_calling/tests/main.nf.test | 63 ++++ .../sample_calling/tests/main.nf.test.snap | 171 ++++++++++ .../pna/{ => v1}/generate_reports/main.nf | 0 .../pna/{ => v1}/generate_reports/meta.yml | 0 subworkflows/local/pna/{ => v1}/main.nf | 59 +++- subworkflows/local/pna/{ => v1}/meta.yml | 0 .../local/pna/{ => v1}/nextflow.config | 0 .../local/pna/{ => v1}/tests/main.nf.test | 0 .../pna/{ => v1}/tests/main.nf.test.snap | 0 .../local/pna/{ => v1}/tests/tags.yml | 0 subworkflows/local/pna/v2/main.nf | 305 ++++++++++++++++++ tests/pna.nf.test | 1 + workflows/pixelator.nf | 73 +---- 14 files changed, 683 insertions(+), 61 deletions(-) create mode 100644 modules/local/pixelator/single-cell-pna/sample_calling/main.nf create mode 100644 modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test create mode 100644 modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap rename subworkflows/local/pna/{ => v1}/generate_reports/main.nf (100%) rename subworkflows/local/pna/{ => v1}/generate_reports/meta.yml (100%) rename subworkflows/local/pna/{ => v1}/main.nf (79%) rename subworkflows/local/pna/{ => v1}/meta.yml (100%) rename subworkflows/local/pna/{ => v1}/nextflow.config (100%) rename subworkflows/local/pna/{ => v1}/tests/main.nf.test (100%) rename subworkflows/local/pna/{ => v1}/tests/main.nf.test.snap (100%) rename subworkflows/local/pna/{ => v1}/tests/tags.yml (100%) create mode 100644 subworkflows/local/pna/v2/main.nf diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf new file mode 100644 index 00000000..96c613e4 --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf @@ -0,0 +1,72 @@ +process PIXELATOR_PNA_SAMPLE_CALLING { + tag "${meta.id}" + label 'process_high' + + // TODO: Add conda + // conda "bioconda::pixelator=0.18.2" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'quay.io/pixelgen-technologies/pixelator:0.25.0' + : 'quay.io/pixelgen-technologies/pixelator:0.25.0'}" + + input: + tuple val(meta), path(data), path(samplesheet) + + output: + tuple val(meta), path("sample_calling/*.pxl"), emit: pixelfile + tuple val(meta), path("sample_calling/*.report.json"), emit: report_json + tuple val(meta), path("sample_calling/*.meta.json"), emit: metadata_json + tuple val(meta), path("sample_calling/*"), emit: all_results + + tuple val(meta), path("*pixelator-sample-calling.log"), emit: log + tuple val('sample_calling'), path("sample_calling/*"), topic: all_results_for_reports + + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + + """ + pixelator \ + --cores ${task.cpus} \ + --log-file ${prefix}.pixelator-sample-calling.log \ + --verbose \ + single-cell-pna \ + sample-calling \ + --samplesheet ${samplesheet} \ + --output . \ + ${args} \ + ${data} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ + + // The stub here generates multiple output pxl files to mimic real run + // in reality these should match up with what has been configured in the + // samplesheet + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + """ + mkdir sample_calling + touch sample_calling/${prefix}.report.json + touch sample_calling/${prefix}.meta.json + touch sample_calling/${prefix}-S1.pxl + touch sample_calling/${prefix}-S2.pxl + touch sample_calling/${prefix}-S3.pxl + touch sample_calling/${prefix}-S4.pxl + touch ${prefix}.pixelator-sample-calling.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test new file mode 100644 index 00000000..44fa9b2c --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process PIXELATOR_PNA_SAMPLE_CALLING" + script "../main.nf" + process "PIXELATOR_PNA_SAMPLE_CALLING" + tag "modules" + tag "pixelator" + tag "pixelator/pna" + tag "pixelator/single_cell_pna_sample_calling" + + test("PNA sample calling - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + ] + """ + } // TODO update test files with intermediary files from hashed run + // Need hashing panels + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("PNA sample calling - small test") { + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + ] + """ + } + } + + then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + process.out.versions_pixelator, + ).match() } + ) + } + } +} diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap new file mode 100644 index 00000000..4044f38a --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap @@ -0,0 +1,171 @@ +{ + "PNA denoise - small test": { + "content": [ + 1, + [ + "pixelator", + "pixelator/denoise", + "pixelator/denoise/PNA055_Sample07_filtered_S7.meta.json", + "pixelator/denoise/PNA055_Sample07_filtered_S7.report.json", + "pixelator/logs", + "pixelator/logs/PNA055_Sample07_filtered_S7", + "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log" + ], + [ + [ + "PIXELATOR_PNA_DENOISE", + "pixelator", + "0.23.0" + ] + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-11T14:06:20.982865336" + }, + "PNA denoise - stub": { + "content": [ + { + "0": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + [ + "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "4": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + "PIXELATOR_PNA_DENOISE", + "pixelator", + "0.23.0" + ] + ], + "all_results": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + [ + "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "log": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metadata_json": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pixelfile": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_json": [ + [ + { + "id": "PNA055_Sample07_filtered_S7", + "design": "pna-2", + "panel": "proxiome-immuno-155-v2", + "technology": "pna" + }, + "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_pixelator": [ + [ + "PIXELATOR_PNA_DENOISE", + "pixelator", + "0.23.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-11T14:06:01.113423824" + } +} \ No newline at end of file diff --git a/subworkflows/local/pna/generate_reports/main.nf b/subworkflows/local/pna/v1/generate_reports/main.nf similarity index 100% rename from subworkflows/local/pna/generate_reports/main.nf rename to subworkflows/local/pna/v1/generate_reports/main.nf diff --git a/subworkflows/local/pna/generate_reports/meta.yml b/subworkflows/local/pna/v1/generate_reports/meta.yml similarity index 100% rename from subworkflows/local/pna/generate_reports/meta.yml rename to subworkflows/local/pna/v1/generate_reports/meta.yml diff --git a/subworkflows/local/pna/main.nf b/subworkflows/local/pna/v1/main.nf similarity index 79% rename from subworkflows/local/pna/main.nf rename to subworkflows/local/pna/v1/main.nf index 88f2042d..cb2ab469 100644 --- a/subworkflows/local/pna/main.nf +++ b/subworkflows/local/pna/v1/main.nf @@ -39,6 +39,8 @@ include { PNA_GENERATE_REPORTS } from '../pna/generate_reports' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' + /* ======================================================================================== IMPORT CUSTOM MODULES/SUBWORKFLOWS @@ -48,16 +50,69 @@ include { PNA_GENERATE_REPORTS } from '../pna/generate_reports' // -workflow PNA { +workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files take: fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] panel_files // channel: [ meta, path(panel_file) | ] main: + + ch_fastq_split = fastq + .groupTuple() + .branch { + meta, fastq -> + single: fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + + // + // MODULE: Concatenate FastQ files from the same sample if required + // + ch_fastq_split.multiple + + ch_cat_fastq = CAT_FASTQ ( ch_fastq_split.multiple ) + .reads + .mix(ch_fastq_split.single) + + // Check that multi lane samples use the same panel file + ch_checked_panel_files = panel_files + .map { meta, data -> [ meta.id, data] } + .groupTuple() + .map { id, data -> + if (!data) { + return [id, []] + } + def unique_panels = data.unique() + if (unique_panels.size() > 1) { + exit 1, "ERROR: Concatenated samples must use the same panel." + } + return [ id, unique_panels[0] ] + } + + ch_cat_panel_files = ch_cat_fastq + .map { meta, _fastqs -> [meta.id, meta] } + .join(ch_checked_panel_files) + .map { _id, meta, panel_files -> [meta, panel_files] } + + ch_fastq_technology_split = ch_cat_fastq + .branch { + meta, data -> + pna: meta.technology == 'pna' + return [ meta, data ] + } + + ch_panel_files_technology_split = ch_cat_panel_files + .branch { + meta, data -> + pna: meta.technology == 'pna' + return [ meta, data ] + } // // MODULE: Run pixelator single-cell-pna amplicon // - PIXELATOR_PNA_AMPLICON ( fastq ) + PIXELATOR_PNA_AMPLICON ( ch_cat_fastq ) ch_amplicon = PIXELATOR_PNA_AMPLICON.out.amplicon // diff --git a/subworkflows/local/pna/meta.yml b/subworkflows/local/pna/v1/meta.yml similarity index 100% rename from subworkflows/local/pna/meta.yml rename to subworkflows/local/pna/v1/meta.yml diff --git a/subworkflows/local/pna/nextflow.config b/subworkflows/local/pna/v1/nextflow.config similarity index 100% rename from subworkflows/local/pna/nextflow.config rename to subworkflows/local/pna/v1/nextflow.config diff --git a/subworkflows/local/pna/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test similarity index 100% rename from subworkflows/local/pna/tests/main.nf.test rename to subworkflows/local/pna/v1/tests/main.nf.test diff --git a/subworkflows/local/pna/tests/main.nf.test.snap b/subworkflows/local/pna/v1/tests/main.nf.test.snap similarity index 100% rename from subworkflows/local/pna/tests/main.nf.test.snap rename to subworkflows/local/pna/v1/tests/main.nf.test.snap diff --git a/subworkflows/local/pna/tests/tags.yml b/subworkflows/local/pna/v1/tests/tags.yml similarity index 100% rename from subworkflows/local/pna/tests/tags.yml rename to subworkflows/local/pna/v1/tests/tags.yml diff --git a/subworkflows/local/pna/v2/main.nf b/subworkflows/local/pna/v2/main.nf new file mode 100644 index 00000000..11d5febb --- /dev/null +++ b/subworkflows/local/pna/v2/main.nf @@ -0,0 +1,305 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ +include { softwareVersionsToYAML } from '../../../nf-core/utils_nfcore_pipeline' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CONFIG FILES +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT LOCAL MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { PIXELATOR_PNA_AMPLICON } from '../../../../modules/local/pixelator/single-cell-pna/amplicon' +include { PIXELATOR_PNA_DEMUX } from '../../../../modules/local/pixelator/single-cell-pna/demux' +include { PIXELATOR_PNA_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/collapse' +include { PIXELATOR_PNA_GRAPH } from '../../../../modules/local/pixelator/single-cell-pna/graph' +include { PIXELATOR_PNA_SAMPLE_CALLING } from '../../../../modules/local/pixelator/single-cell-pna/sample_calling' +include { PIXELATOR_PNA_DENOISE } from '../../../../modules/local/pixelator/single-cell-pna/denoise' +include { PIXELATOR_PNA_ANALYSIS } from '../../../../modules/local/pixelator/single-cell-pna/analysis' +include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/combine_collapse' +include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout' + + +include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main.nf' +include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main.nf' + +def pick_file_from_channel(channel) { + channel.map { _meta, file -> file } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT LOCAL SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT NF-CORE MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +/* +======================================================================================== + IMPORT CUSTOM MODULES/SUBWORKFLOWS +======================================================================================== +*/ + +// + + +workflow PIXELATOR_PNA_V2 { + take: + ch_fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] + ch_panel_files // channel: [ meta, path(panel_file) | ] + + main: + ch_versions = Channel.empty() + + + ch_fastq_grouped_by_pool = ch_fastq + .map { meta, fq -> tuple(meta.pool, [meta, fq]) } + .groupTuple() + .map { _pool, list -> + def meta = list[0][0].clone() + meta.id = meta.pool + def fq = (list as List).collect { item -> item[1] } + [meta, fq.unique()] + } + + ch_fastq_split = ch_fastq_grouped_by_pool + .branch { + meta, fastq -> + single: fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + + // + // MODULE: Concatenate FastQ files from the same sample if required + // + + ch_cat_fastq = CAT_FASTQ ( ch_fastq_split.multiple ) + .reads + .mix(ch_fastq_split.single) + + // Remap panel files to use pool as id + ch_panel_files_grouped_by_pool = ch_panel_files + .map { meta, panel_file_path -> tuple(meta.pool, [meta, panel_file_path]) } + .groupTuple() + .map { _pool, list -> + def meta = list[0][0].clone() + meta.id = meta.pool + def panel_file = list[0][1] + [meta, panel_file] + } + + + // Check that multi lane samples use the same panel file + ch_checked_panel_files = ch_panel_files_grouped_by_pool + .map { meta, data -> [ meta.id, data] } + .groupTuple() + .map { id, data -> + if (!data) { + return [id, []] + } + def unique_panels = data.unique() + if (unique_panels.size() > 1) { + exit 1, "ERROR: Concatenated samples must use the same panel." + } + return [ id, unique_panels[0] ] + } + + ch_cat_panel_files = ch_cat_fastq + .map { meta, _fastq -> [meta.id, meta] } + .join(ch_checked_panel_files) + .map { id, meta, panel_files -> [meta, panel_files] } + + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) + + + + // + // MODULE: Run pixelator single-cell-pna amplicon + // + PIXELATOR_PNA_AMPLICON ( ch_cat_fastq ) + ch_amplicon = PIXELATOR_PNA_AMPLICON.out.amplicon + ch_versions = ch_versions.mix(PIXELATOR_PNA_AMPLICON.out.versions.first()) + + // + // MODULE: Run pixelator single-cell demux + // + ch_demux_input = ch_amplicon + .join(ch_panel_files_grouped_by_pool) + .map { meta, fq, panel_file -> [meta, fq, panel_file, meta.panel, meta.design] } + + + PIXELATOR_PNA_DEMUX(ch_demux_input) + ch_demuxed = PIXELATOR_PNA_DEMUX.out.demuxed + ch_versions = ch_versions.mix(PIXELATOR_PNA_DEMUX.out.versions.first()) + + // + // MODULE: Run pixelator single-cell collapse + // + ch_collapse_input = ch_demuxed + .join(ch_panel_files_grouped_by_pool) + .map { meta, parquet, panel_file -> + // Inject the number of parts into the meta data + // to be able to group the files without waiting later + def newMeta = meta.clone() + newMeta['parts'] = parquet.size() + parquet.collect { single_parquet_file -> + [newMeta, single_parquet_file, panel_file, panel_file ? null : meta.panel, meta.design] + } + } + .flatMap() + + + PIXELATOR_PNA_COLLAPSE(ch_collapse_input) + ch_collapsed = PIXELATOR_PNA_COLLAPSE.out.collapsed + ch_collapsed_reports = PIXELATOR_PNA_COLLAPSE.out.report_json + ch_versions = ch_versions.mix(PIXELATOR_PNA_COLLAPSE.out.versions.first()) + + // Collect the partitioned collapse.parquet files in a list per sample + // use the dynamic size information from `meta.parts` to group the files + ch_collapse_collected = ch_collapsed + .join(ch_collapsed_reports) + .map { meta, collapsed, reports -> tuple(groupKey(meta.id, meta.parts), [meta, collapsed, reports]) } + .groupTuple() + .map { _key, data -> + // Remove the parts meta key again + def newMeta = data[0][0].clone() + newMeta.remove('parts') + + // Strip the duplicates meta from each element + def parquet = data.collect { it[1] }.flatten() + def reports = data.collect { it[2] }.flatten() + [newMeta, parquet, reports] + } + + ch_collapse_combine_split = ch_collapse_collected.branch { + single: it[1].size() == 1 + multi: it[1].size() > 1 + } + + + PIXELATOR_PNA_COMBINE_COLLAPSE(ch_collapse_combine_split.multi) + + ch_combined_collapsed = ch_collapse_combine_split.single + .map { meta, parquet, _reports -> [meta, parquet] } + .mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.parquet) + + ch_versions = ch_versions.mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.versions.first()) + + // + // MODULE: Run pixelator single-cell graph + // + ch_graph_input = ch_combined_collapsed + .join(ch_panel_files_grouped_by_pool) + .map { meta, parquet, panel_file -> [meta, parquet, panel_file, panel_file ? null : meta.panel] } + + PIXELATOR_PNA_GRAPH(ch_graph_input) + ch_graph = PIXELATOR_PNA_GRAPH.out.pixelfile + ch_versions = ch_versions.mix(PIXELATOR_PNA_GRAPH.out.versions.first()) + + // + // MODULE: Run pixelator single-cell sample-calling + // + ch_sample_calling_input = ch_graph + .map { meta, parquet -> [meta, parquet, file(params.input)] } + + PIXELATOR_PNA_SAMPLE_CALLING (ch_sample_calling_input) + ch_sample_called = PIXELATOR_PNA_SAMPLE_CALLING.out.pixelfile + ch_versions = ch_versions.mix(PIXELATOR_PNA_SAMPLE_CALLING.out.versions.first()) + + + // Extract the sample names from the pixel file names so that we can + // merge them in with the panel file names correctly + // Also filter out the undetermined samples here + ch_sample_called = ch_sample_called + .flatMap { meta, pxl_files -> + def files = pxl_files instanceof List ? pxl_files : [pxl_files] + files.findAll { file -> !file.getName().contains('undetermined') } + .collect { + file -> + def new_meta = meta.clone() + new_meta.id = file.getName().replace('.dehashed.pxl', '') + [new_meta, file] + } + } + + // + // MODULE: Run pixelator single-cell denoise + // + PIXELATOR_PNA_DENOISE ( ch_sample_called ) + ch_denoise = PIXELATOR_PNA_DENOISE.out.pixelfile + ch_versions = ch_versions.mix(PIXELATOR_PNA_DENOISE.out.versions.first()) + + // + // MODULE: Run pixelator single-cell analysis + // + ch_analysis_input = params.skip_denoise ? ch_sample_called : ch_denoise + PIXELATOR_PNA_ANALYSIS ( ch_analysis_input ) + ch_analysis = PIXELATOR_PNA_ANALYSIS.out.pixelfile + ch_versions = ch_versions.mix(PIXELATOR_PNA_ANALYSIS.out.versions.first()) + + // + // MODULE: Run pixelator single-cell layout + // + + PIXELATOR_PNA_LAYOUT( ch_analysis ) + ch_versions = ch_versions.mix(PIXELATOR_PNA_LAYOUT.out.versions.first()) + + // Prepare all data needed by reporting for each pixelator step + ch_input = channel.fromPath(params.input) + ch_all_results_grouped = channel + .topic('all_results_for_reports') + .map{ stage, files -> { + tuple(stage, files) + }} + .groupTuple() + + ch_all_results_split_by_stage = ch_all_results_grouped.branch { topic, _files -> + amplicon: topic == 'amplicon' + demux: topic == 'demux' + collapse: topic == 'collapse' + graph: topic == 'graph' + sample_calling: topic == 'sample_calling' + denoise: topic == 'denoise' + analysis: topic == 'analysis' + post_analysis: topic == 'post_analysis' + layout: topic == 'layout' + } + + def pick_file_from_channel = { channel -> + channel.map { _topic, files -> files.flatten() } + } + + if (!params.skip_experiment_summary) { + EXPERIMENT_SUMMARY( + ch_input, + pick_file_from_channel(ch_all_results_split_by_stage.amplicon), + pick_file_from_channel(ch_all_results_split_by_stage.demux), + pick_file_from_channel(ch_all_results_split_by_stage.collapse), + pick_file_from_channel(ch_all_results_split_by_stage.graph), + pick_file_from_channel(ch_all_results_split_by_stage.sample_calling), + pick_file_from_channel(ch_all_results_split_by_stage.denoise), + pick_file_from_channel(ch_all_results_split_by_stage.analysis), + pick_file_from_channel(ch_all_results_split_by_stage.layout), + ) + } + + emit: + versions = ch_versions + graph = ch_graph + analysis = ch_analysis +} diff --git a/tests/pna.nf.test b/tests/pna.nf.test index 5652b11e..e00fa0f2 100644 --- a/tests/pna.nf.test +++ b/tests/pna.nf.test @@ -19,6 +19,7 @@ nextflow_pipeline { pna_graph_component_size_min_threshold = 100 skip_experiment_summary = false save_all = true + technology = "pna_v1" } } diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index 8a56e923..ffc4aecc 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -23,7 +23,8 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pixe // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { PNA } from '../subworkflows/local/pna' +include { PIXELATOR_PNA_V1 } from '../subworkflows/local/pna/v1' +include { PIXELATOR_PNA_V2 } from '../subworkflows/local/pna/v2' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39,8 +40,6 @@ include { PNA } from '../subworkflows/local/pna' IMPORT CUSTOM MODULES/SUBWORKFLOWS ======================================================================================== */ -include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' - /* ======================================================================================== @@ -64,64 +63,20 @@ workflow PIXELATOR { ch_reads = ch_samplesheet.map { meta, _panel, reads -> [ meta, reads ] } ch_panel_files = ch_samplesheet.map { meta, panel, _reads -> [ meta, panel ] } - ch_fastq_split = ch_reads - .groupTuple() - .branch { - meta, fastq -> - single: fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - - // - // MODULE: Concatenate FastQ files from the same sample if required - // - ch_fastq_split.multiple - - ch_cat_fastq = CAT_FASTQ ( ch_fastq_split.multiple ) - .reads - .mix(ch_fastq_split.single) - - // Check that multi lane samples use the same panel file - ch_checked_panel_files = ch_panel_files - .map { meta, data -> [ meta.id, data] } - .groupTuple() - .map { id, data -> - if (!data) { - return [id, []] - } - def unique_panels = data.unique() - if (unique_panels.size() > 1) { - exit 1, "ERROR: Concatenated samples must use the same panel." - } - return [ id, unique_panels[0] ] - } - - ch_cat_panel_files = ch_cat_fastq - .map { meta, _fastqs -> [meta.id, meta] } - .join(ch_checked_panel_files) - .map { _id, meta, panel_files -> [meta, panel_files] } - - ch_fastq_technology_split = ch_cat_fastq - .branch { - meta, data -> - pna: meta.technology == 'pna' - return [ meta, data ] - } - - ch_panel_files_technology_split = ch_cat_panel_files - .branch { - meta, data -> - pna: meta.technology == 'pna' - return [ meta, data ] + if (params.technology == "pna_v1") { + PIXELATOR_PNA_V1( + ch_reads, + ch_panel_files + ) + } else if (params.technology == "pna_v2") { + PIXELATOR_PNA_V2( + ch_reads, + ch_panel_files + ) + } else { + error "Unknown technology: \"${params.technology}\"" } - PNA( - ch_fastq_technology_split.pna, - ch_panel_files_technology_split.pna - ) - // // Collate and save software versions // From 6707d908a96522c1135aff3c548c1c88cdebde2d Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 6 May 2026 08:38:04 +0200 Subject: [PATCH 29/90] Make ES take all files in one channel --- CHANGELOG.md | 2 +- modules/local/experiment_summary/main.nf | 28 ++--- modules/local/experiment_summary/meta.yml | 30 +----- .../experiment_summary/tests/main.nf.test | 56 ++++------ .../tests/main.nf.test.snap | 4 +- .../single-cell-pna/amplicon/main.nf | 1 + .../single-cell-pna/analysis/main.nf | 1 + .../single-cell-pna/collapse/main.nf | 1 + .../single-cell-pna/combine_collapse/main.nf | 1 + .../pixelator/single-cell-pna/demux/main.nf | 1 + .../pixelator/single-cell-pna/denoise/main.nf | 1 + .../pixelator/single-cell-pna/graph/main.nf | 1 + .../pixelator/single-cell-pna/layout/main.nf | 1 + .../single-cell-pna/sample_calling/main.nf | 4 +- nextflow_schema.json | 6 ++ .../local/pna/v1/generate_reports/main.nf | 95 ---------------- .../local/pna/v1/generate_reports/meta.yml | 83 -------------- subworkflows/local/pna/v1/main.nf | 102 +++++++----------- subworkflows/local/pna/v2/main.nf | 63 +++-------- .../utils_nfcore_pixelator_pipeline/main.nf | 20 ---- tests/pna.nf.test.snap | 4 +- workflows/pixelator.nf | 4 +- 22 files changed, 113 insertions(+), 396 deletions(-) delete mode 100644 subworkflows/local/pna/v1/generate_reports/main.nf delete mode 100644 subworkflows/local/pna/v1/generate_reports/meta.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a01e2be..e5754ab9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ------------- | ----------- | ----------- | -| `pixelatorES` | 0.6.0 | 0.8.6 | +| `pixelatorES` | 0.6.0 | 0.9.0 | | `pixelatorES` | 0.23.0 | 0.26.0 | ### Parameters diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index e426544f..bd3b42b2 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -4,21 +4,12 @@ process EXPERIMENT_SUMMARY { label "error_retry" container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelatores:0.8.6' - : 'quay.io/pixelgen-technologies/pixelatores:0.8.6'}" + ? 'quay.io/pixelgen-technologies/pixelatores:0.10.1' + : 'quay.io/pixelgen-technologies/pixelatores:0.10.1'}" input: path samplesheet_path - tuple ( - val(meta), - path(amplicon_data , stageAs: "results/amplicon/*"), - path(demux_data , stageAs: "results/demux/*"), - path(collapse_data , stageAs: "results/collapse/*"), - path(graph_data , stageAs: "results/graph/*"), - path(denoise_data , stageAs: "results/denoise/*"), - path(analysis_data , stageAs: "results/analysis/*"), - path(layout_data , stageAs: "results/layout/*") - ) + tuple val(meta), val(result_stages), path(results_data, arity: "1..*", stageAs: "results_raw/?/*") output: tuple val(meta), path("*experiment-summary.html") , emit: html @@ -26,9 +17,22 @@ process EXPERIMENT_SUMMARY { script: def args = task.ext.args ?: '' + + assert result_stages instanceof List : "Expected result_stages to be a List, got ${result_stages?.getClass()?.simpleName ?: 'null'}" + assert results_data instanceof List : "Expected results_data to be a List, got ${results_data?.getClass()?.simpleName ?: 'null'}" + assert results_data.size() == result_stages.size(): "Mismatch between result files (${results_data.size()}) and stage labels (${result_stages.size()})" + + def stageCopies = [result_stages, results_data].transpose().collect { stage, file -> + """ + mkdir -p "results/${stage}" + ln -s "../../${file}" "results/${stage}/" + """ + }.join('\n') """ # Copy the full quarto dir from the read-only image into the workdir cp -r /workspace/inst/quarto/ ./quarto/ + mkdir -p results + ${stageCopies} quarto render ./quarto/pixelatorES.qmd \\ -P sample_sheet="\$PWD/${samplesheet_path}" \\ -P data_folder="\$PWD/results/" \\ diff --git a/modules/local/experiment_summary/meta.yml b/modules/local/experiment_summary/meta.yml index c6ed379d..46509e73 100644 --- a/modules/local/experiment_summary/meta.yml +++ b/modules/local/experiment_summary/meta.yml @@ -23,33 +23,13 @@ input: description: | Groovy Map containing sample information e.g. [ id:'sample1' ] - - amplicon_data: - type: file - description: Inputs staged under results/amplicon. - ontologies: [] - - demux_data: - type: file - description: Inputs staged under results/demux. - ontologies: [] - - collapse_data: - type: file - description: Inputs staged under results/collapse. - ontologies: [] - - graph_data: - type: file - description: Inputs staged under results/graph. - ontologies: [] - - denoise_data: - type: file - description: Inputs staged under results/denoise. - ontologies: [] - - analysis_data: - type: file - description: Inputs staged under results/analysis. + - result_stages: + type: list + description: Stage label for each file in `results_data` (same order). ontologies: [] - - layout_data: + - results_data: type: file - description: Inputs staged under results/layout. + description: Result files to organize under stage folders in the report input. ontologies: [] output: html: diff --git a/modules/local/experiment_summary/tests/main.nf.test b/modules/local/experiment_summary/tests/main.nf.test index a78dc744..55761e46 100644 --- a/modules/local/experiment_summary/tests/main.nf.test +++ b/modules/local/experiment_summary/tests/main.nf.test @@ -20,50 +20,40 @@ nextflow_process { input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna.csv', checkIfExists: true) ] input[1] = [ [id:'all', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - // amplicon + [ + 'amplicon', 'amplicon', 'amplicon', 'amplicon', + 'demux', 'demux', 'demux', 'demux', + 'collapse', 'collapse', 'collapse', 'collapse', + 'graph', 'graph', 'graph', 'graph', + 'denoise', 'denoise', 'denoise', 'denoise', + 'analysis', 'analysis', 'analysis', 'analysis', + 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', + ], [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // demux - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // (combined collapse) - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // graph - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // denoise - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // analysis - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // layout - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.layout.pxl', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), @@ -100,50 +90,40 @@ nextflow_process { input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna.csv', checkIfExists: true) ] input[1] = [ [id:'all', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - // amplicon + [ + 'amplicon', 'amplicon', 'amplicon', 'amplicon', + 'demux', 'demux', 'demux', 'demux', + 'collapse', 'collapse', 'collapse', 'collapse', + 'graph', 'graph', 'graph', 'graph', + 'denoise', 'denoise', 'denoise', 'denoise', + 'analysis', 'analysis', 'analysis', 'analysis', + 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', + ], [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // demux - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // (combined collapse) - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // graph - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // denoise - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // analysis - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - ], - // layout - [ file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.layout.pxl', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 0fb5fb0b..4dd334b6 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -10,7 +10,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.8.6 " + "0.9.0 " ] ] ], @@ -26,7 +26,7 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.8.6 " + "0.9.0 " ] ] ], diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/single-cell-pna/amplicon/main.nf index 378e661a..7b40ad9e 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/main.nf +++ b/modules/local/pixelator/single-cell-pna/amplicon/main.nf @@ -16,6 +16,7 @@ process PIXELATOR_PNA_AMPLICON { tuple val(meta), path("amplicon/*.report.json"), emit: report_json tuple val(meta), path("amplicon/*.meta.json"), emit: metadata_json tuple val(meta), path("*pixelator-amplicon.log"), emit: log + tuple val('amplicon'), path("amplicon/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/analysis/main.nf b/modules/local/pixelator/single-cell-pna/analysis/main.nf index 90fe224e..b9c776e7 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/main.nf +++ b/modules/local/pixelator/single-cell-pna/analysis/main.nf @@ -18,6 +18,7 @@ process PIXELATOR_PNA_ANALYSIS { tuple val(meta), path("analysis/*.meta.json"), emit: metadata_json tuple val(meta), path("analysis/*"), emit: all_results tuple val(meta), path("*pixelator-analysis.log"), emit: log + tuple val('analysis'), path("analysis/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/collapse/main.nf b/modules/local/pixelator/single-cell-pna/collapse/main.nf index 6fc43487..510783ee 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/collapse/main.nf @@ -18,6 +18,7 @@ process PIXELATOR_PNA_COLLAPSE { tuple val(meta), path("collapse/*.report.json", arity: '1..*'), emit: report_json tuple val(meta), path("collapse/*.meta.json"), emit: metadata_json tuple val(meta), path("*pixelator-collapse.log"), emit: log + tuple val('collapse'), path("collapse/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf index c16bf0d0..a683dabe 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf @@ -17,6 +17,7 @@ process PIXELATOR_PNA_COMBINE_COLLAPSE { tuple val(meta), path("collapse/*.report.json"), emit: report_json tuple val(meta), path("collapse/*.meta.json"), emit: metadata_json tuple val(meta), path("*pixelator-combine-collapse.log"), emit: log + tuple val('collapse'), path("collapse/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/demux/main.nf b/modules/local/pixelator/single-cell-pna/demux/main.nf index b8ca5407..5703b013 100644 --- a/modules/local/pixelator/single-cell-pna/demux/main.nf +++ b/modules/local/pixelator/single-cell-pna/demux/main.nf @@ -19,6 +19,7 @@ process PIXELATOR_PNA_DEMUX { tuple val(meta), path("demux/*.report.json"), emit: report_json tuple val(meta), path("demux/*.meta.json"), emit: metadata_json tuple val(meta), path("*pixelator-demux.log"), emit: log + tuple val('demux'), path("demux/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/denoise/main.nf b/modules/local/pixelator/single-cell-pna/denoise/main.nf index 337df233..fecb1385 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/main.nf +++ b/modules/local/pixelator/single-cell-pna/denoise/main.nf @@ -18,6 +18,7 @@ process PIXELATOR_PNA_DENOISE { tuple val(meta), path("denoise/*.meta.json") , emit: metadata_json tuple val(meta), path("denoise/*") , emit: all_results tuple val(meta), path("*pixelator-denoise.log") , emit: log + tuple val('denoise'), path("denoise/*") , topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/graph/main.nf b/modules/local/pixelator/single-cell-pna/graph/main.nf index fb49f8c8..c02b63bf 100644 --- a/modules/local/pixelator/single-cell-pna/graph/main.nf +++ b/modules/local/pixelator/single-cell-pna/graph/main.nf @@ -16,6 +16,7 @@ process PIXELATOR_PNA_GRAPH { tuple val(meta), path("graph/*.report.json"), emit: report_json tuple val(meta), path("graph/*.meta.json"), emit: metadata_json tuple val(meta), path("*pixelator-graph.log"), emit: log + tuple val('graph'), path("graph/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/layout/main.nf b/modules/local/pixelator/single-cell-pna/layout/main.nf index 3b565a50..7e98cf34 100644 --- a/modules/local/pixelator/single-cell-pna/layout/main.nf +++ b/modules/local/pixelator/single-cell-pna/layout/main.nf @@ -18,6 +18,7 @@ process PIXELATOR_PNA_LAYOUT { tuple val(meta), path("layout/*"), emit: all_results tuple val(meta), path("*pixelator-layout.log"), emit: log + tuple val('layout'), path("layout/*"), topic: all_results_for_reports tuple val("${task.process}"), val('pixelator'), eval("pixelator --version 2>/dev/null | sed 's/pixelator, version //g'"), emit: versions_pixelator, topic: versions diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf index 96c613e4..885f4601 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf +++ b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_PNA_SAMPLE_CALLING { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.25.0' - : 'quay.io/pixelgen-technologies/pixelator:0.25.0'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.26.0' + : 'quay.io/pixelgen-technologies/pixelator:0.26.0'}" input: tuple val(meta), path(data), path(samplesheet) diff --git a/nextflow_schema.json b/nextflow_schema.json index 0bf50ca5..73b52c16 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -415,6 +415,12 @@ "type": "boolean", "default": true, "description": "Save all JSON report and metadata files generated by pixelator." + }, + "technology": { + "type": "string", + "description": "The technology used to process the samples", + "enum": ["proxiome-v1", "proxiome-v2", "hashed_samples", "nonhashed_samples"], + "default": "proxiome-v1" } } }, diff --git a/subworkflows/local/pna/v1/generate_reports/main.nf b/subworkflows/local/pna/v1/generate_reports/main.nf deleted file mode 100644 index 92198906..00000000 --- a/subworkflows/local/pna/v1/generate_reports/main.nf +++ /dev/null @@ -1,95 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main' - -/* -======================================================================================== - SUBWORKFLOW TO GENERATE PIXELATOR REPORTS -======================================================================================== -*/ - -workflow PNA_GENERATE_REPORTS { - take: - samplesheet // channel: [path(samplesheet)] - panel_files // channel: [meta, path(panel_file) | []] - amplicon_data // channel: [meta, [path, ...]] - demux_data // channel: [meta, [path, ...]] - collapse_data // channel: [meta, [path, ...]] - graph_data // channel: [meta, [path, ...]] - denoise_data // channel: [meta, [path, ...]] - analysis_data // channel: [meta, [path, ...]] - layout_data // channel: [meta, [path, ...]] - - skip_experiment_summary // boolean - - main: - ch_meta_col = panel_files - .map { meta, _data -> [meta.id, meta] } - .groupTuple() - .map { id, data -> - if (data instanceof List) { - def combined_meta = [:] - data.each { meta -> combined_meta += meta } - return [id, combined_meta] - } - return [id, data] - } - - ch_report_data = ch_meta_col - .join( panel_files.map { meta, data -> [ meta.id, data ] } ) - .join( amplicon_data.map { meta, data -> [ meta.id, data ] } ) - .join( demux_data.map { meta, data -> [ meta.id, data ] } ) - .join( collapse_data.map { meta, data -> [ meta.id, data ] } ) - .join( graph_data.map { meta, data -> [ meta.id, data ] } ) - .join( denoise_data.map { meta, data -> [ meta.id, data ] } ) - .join( analysis_data.map { meta, data -> [ meta.id, data ] } ) - .join( layout_data.map { meta, data -> [ meta.id, data ] } ) - - - - - // Accumulate results across all samples grouped per stage - - def accumulator = [ - meta: [ id: "all-samples", samples: [] ], - amplicon: [], - demux: [], - collapse: [], - graph: [], - denoise: [], - analysis: [], - layout: [] - ] - - ch_grouped_data = ch_report_data.reduce ( accumulator ) { acc, val -> - def (_id, meta, _panels, amplicon, demux, collapse, graph, denoise, analysis, layout) = val - acc.meta.samples += meta.id - acc.amplicon += amplicon - acc.demux += demux - acc.collapse += collapse - acc.graph += graph - acc.denoise += denoise - acc.analysis += analysis - acc.layout += layout - return acc - }.map { acc -> - [ acc.meta, acc.amplicon, acc.demux, acc.collapse, acc.graph, acc.denoise, acc.analysis, acc.layout ] - } - // Filter out the entry if it just contains empty lists, eg when no PNA samples are present - .filter { it -> it[0].samples.size() > 0 } - - if (!skip_experiment_summary) { - EXPERIMENT_SUMMARY ( samplesheet, ch_grouped_data ) - ch_experiment_summary = EXPERIMENT_SUMMARY.out.html - } else { - ch_experiment_summary = ch_grouped_data.map { it -> it[0] }.combine(channel.of([])) - } - - - emit: - experiment_summary = ch_experiment_summary -} diff --git a/subworkflows/local/pna/v1/generate_reports/meta.yml b/subworkflows/local/pna/v1/generate_reports/meta.yml deleted file mode 100644 index 7fac5b6c..00000000 --- a/subworkflows/local/pna/v1/generate_reports/meta.yml +++ /dev/null @@ -1,83 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: pna_generate_reports -description: Aggregate Pixelator stage outputs and generate an experiment summary report. -keywords: - - pixelator - - pna - - report - - summary -components: - - experiment/summary -input: - - samplesheet: - type: file - description: | - Input channel containing the sample sheet path. - Structure: [ path(samplesheet) ] - pattern: "*.{csv,tsv,txt}" - - panel_files: - type: file - description: | - Input channel containing panel files per sample. - Structure: [ val(meta), path(panel_file) ] - pattern: "*" - - amplicon_data: - type: file - description: | - Input channel with amplicon report and metadata files per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*.{json,meta.json,report.json}" - - demux_data: - type: file - description: | - Input channel with demux report and metadata files per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*.{json,meta.json,report.json}" - - collapse_data: - type: file - description: | - Input channel with collapse report and metadata files per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*.{json,meta.json,report.json}" - - graph_data: - type: file - description: | - Input channel with graph outputs per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*" - - denoise_data: - type: file - description: | - Input channel with denoise outputs per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*" - - analysis_data: - type: file - description: | - Input channel with analysis outputs per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*" - - layout_data: - type: file - description: | - Input channel with layout report and metadata files per sample. - Structure: [ val(meta), [ path(file), ... ] ] - pattern: "*.{json,meta.json,report.json}" - - skip_experiment_summary: - type: boolean - description: Boolean flag controlling whether experiment summary generation is skipped. -output: - - experiment_summary: - type: file - description: | - Channel containing experiment summary HTML files when enabled, or empty placeholders when skipped. - Structure: [ val(meta), path("*.html") ] - pattern: "*.html" -authors: - - "@Aratz" - - "@johandahlberg" - - "@fbdtemme" -maintainers: - - "@Aratz" - - "@johandahlberg" - - "@fbdtemme" diff --git a/subworkflows/local/pna/v1/main.nf b/subworkflows/local/pna/v1/main.nf index cb2ab469..10a00ea1 100644 --- a/subworkflows/local/pna/v1/main.nf +++ b/subworkflows/local/pna/v1/main.nf @@ -16,14 +16,15 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PIXELATOR_PNA_AMPLICON } from '../../../modules/local/pixelator/single-cell-pna/amplicon/main' -include { PIXELATOR_PNA_DEMUX } from '../../../modules/local/pixelator/single-cell-pna/demux/main' -include { PIXELATOR_PNA_COLLAPSE } from '../../../modules/local/pixelator/single-cell-pna/collapse/main' -include { PIXELATOR_PNA_GRAPH } from '../../../modules/local/pixelator/single-cell-pna/graph/main' -include { PIXELATOR_PNA_DENOISE } from '../../../modules/local/pixelator/single-cell-pna/denoise/main' -include { PIXELATOR_PNA_ANALYSIS } from '../../../modules/local/pixelator/single-cell-pna/analysis/main' -include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../modules/local/pixelator/single-cell-pna/combine_collapse/main' -include { PIXELATOR_PNA_LAYOUT } from '../../../modules/local/pixelator/single-cell-pna/layout/main' +include { PIXELATOR_PNA_AMPLICON } from '../../../../modules/local/pixelator/single-cell-pna/amplicon/main' +include { PIXELATOR_PNA_DEMUX } from '../../../../modules/local/pixelator/single-cell-pna/demux/main' +include { PIXELATOR_PNA_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/collapse/main' +include { PIXELATOR_PNA_GRAPH } from '../../../../modules/local/pixelator/single-cell-pna/graph/main' +include { PIXELATOR_PNA_DENOISE } from '../../../../modules/local/pixelator/single-cell-pna/denoise/main' +include { PIXELATOR_PNA_ANALYSIS } from '../../../../modules/local/pixelator/single-cell-pna/analysis/main' +include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/combine_collapse/main' +include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout/main' +include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main.nf' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -31,15 +32,13 @@ include { PIXELATOR_PNA_LAYOUT } from '../../../modules/local/pixelato ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PNA_GENERATE_REPORTS } from '../pna/generate_reports' - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-CORE MODULES/SUBWORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' +include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main' /* ======================================================================================== @@ -52,12 +51,12 @@ include { CAT_FASTQ } from '../../../modules/nf-core/cat/fas workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files take: - fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] - panel_files // channel: [ meta, path(panel_file) | ] + ch_fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] + ch_panel_files // channel: [ meta, path(panel_file) | ] main: - ch_fastq_split = fastq + ch_fastq_split = ch_fastq .groupTuple() .branch { meta, fastq -> @@ -77,7 +76,7 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files .mix(ch_fastq_split.single) // Check that multi lane samples use the same panel file - ch_checked_panel_files = panel_files + ch_checked_panel_files = ch_panel_files .map { meta, data -> [ meta.id, data] } .groupTuple() .map { id, data -> @@ -96,19 +95,6 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files .join(ch_checked_panel_files) .map { _id, meta, panel_files -> [meta, panel_files] } - ch_fastq_technology_split = ch_cat_fastq - .branch { - meta, data -> - pna: meta.technology == 'pna' - return [ meta, data ] - } - - ch_panel_files_technology_split = ch_cat_panel_files - .branch { - meta, data -> - pna: meta.technology == 'pna' - return [ meta, data ] - } // // MODULE: Run pixelator single-cell-pna amplicon // @@ -119,7 +105,7 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files // MODULE: Run pixelator single-cell demux // ch_demux_input = ch_amplicon - .join(panel_files) + .join(ch_panel_files) .map { meta, fq, panel_file -> [meta, fq, panel_file, meta.panel, meta.design] } @@ -130,7 +116,7 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files // MODULE: Run pixelator single-cell collapse // ch_collapse_input = ch_demuxed - .join(panel_files) + .join(ch_panel_files) .map { meta, parquet, panel_file -> // Inject the number of parts into the meta data // to be able to group the files without waiting later @@ -181,7 +167,7 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files // MODULE: Run pixelator single-cell graph // ch_graph_input = ch_combined_collapsed - .join(panel_files) + .join(ch_panel_files) .map { meta, parquet, panel_file -> [meta, parquet, panel_file, panel_file ? null : meta.panel] } PIXELATOR_PNA_GRAPH(ch_graph_input) @@ -207,42 +193,28 @@ workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files PIXELATOR_PNA_LAYOUT(ch_analysis) // Prepare all data needed by reporting for each pixelator step - - ch_amplicon_data = PIXELATOR_PNA_AMPLICON.out.report_json - .concat(PIXELATOR_PNA_AMPLICON.out.metadata_json) - .groupTuple(size: 2) - - ch_demux_data = PIXELATOR_PNA_DEMUX.out.report_json - .concat(PIXELATOR_PNA_DEMUX.out.metadata_json) - .groupTuple(size: 2) - - ch_collapse_data = PIXELATOR_PNA_COMBINE_COLLAPSE.out.report_json - .concat(PIXELATOR_PNA_COMBINE_COLLAPSE.out.metadata_json) - .groupTuple(size: 2) - - ch_cluster_data = PIXELATOR_PNA_GRAPH.out.all_results - ch_denoise_data = PIXELATOR_PNA_DENOISE.out.all_results - ch_analysis_data = PIXELATOR_PNA_ANALYSIS.out.all_results - - ch_layout_data = PIXELATOR_PNA_LAYOUT.out.report_json - .concat(PIXELATOR_PNA_LAYOUT.out.metadata_json) - .groupTuple(size: 2) - - ch_input = channel.fromPath(params.input) + ch_experiment_summary_input = channel + .topic('all_results_for_reports') + .map { stage, files -> + def values = files instanceof List ? files : [files] + values.collect { f -> tuple(stage, f) } + } + .flatMap { it } + .collect(flat: false) + .map { stageFilePairs -> + def meta = [id: 'all'] + def stages = stageFilePairs.collect { it[0] } + def files = stageFilePairs.collect { it[1] } + tuple(meta, stages, files) + } - PNA_GENERATE_REPORTS( - ch_input, - panel_files, - ch_amplicon_data, - ch_demux_data, - ch_collapse_data, - ch_cluster_data, - ch_denoise_data, - ch_analysis_data, - ch_layout_data, - params.skip_experiment_summary - ) + if (!params.skip_experiment_summary) { + EXPERIMENT_SUMMARY( + ch_input, + ch_experiment_summary_input, + ) + } emit: graph = ch_graph diff --git a/subworkflows/local/pna/v2/main.nf b/subworkflows/local/pna/v2/main.nf index 11d5febb..f5417ba2 100644 --- a/subworkflows/local/pna/v2/main.nf +++ b/subworkflows/local/pna/v2/main.nf @@ -31,10 +31,6 @@ include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixel include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main.nf' include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main.nf' -def pick_file_from_channel(channel) { - channel.map { _meta, file -> file } -} - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL SUBWORKFLOWS @@ -124,16 +120,11 @@ workflow PIXELATOR_PNA_V2 { .join(ch_checked_panel_files) .map { id, meta, panel_files -> [meta, panel_files] } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) - - - // // MODULE: Run pixelator single-cell-pna amplicon // PIXELATOR_PNA_AMPLICON ( ch_cat_fastq ) ch_amplicon = PIXELATOR_PNA_AMPLICON.out.amplicon - ch_versions = ch_versions.mix(PIXELATOR_PNA_AMPLICON.out.versions.first()) // // MODULE: Run pixelator single-cell demux @@ -145,7 +136,6 @@ workflow PIXELATOR_PNA_V2 { PIXELATOR_PNA_DEMUX(ch_demux_input) ch_demuxed = PIXELATOR_PNA_DEMUX.out.demuxed - ch_versions = ch_versions.mix(PIXELATOR_PNA_DEMUX.out.versions.first()) // // MODULE: Run pixelator single-cell collapse @@ -167,7 +157,6 @@ workflow PIXELATOR_PNA_V2 { PIXELATOR_PNA_COLLAPSE(ch_collapse_input) ch_collapsed = PIXELATOR_PNA_COLLAPSE.out.collapsed ch_collapsed_reports = PIXELATOR_PNA_COLLAPSE.out.report_json - ch_versions = ch_versions.mix(PIXELATOR_PNA_COLLAPSE.out.versions.first()) // Collect the partitioned collapse.parquet files in a list per sample // use the dynamic size information from `meta.parts` to group the files @@ -198,8 +187,6 @@ workflow PIXELATOR_PNA_V2 { .map { meta, parquet, _reports -> [meta, parquet] } .mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.parquet) - ch_versions = ch_versions.mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.versions.first()) - // // MODULE: Run pixelator single-cell graph // @@ -209,7 +196,6 @@ workflow PIXELATOR_PNA_V2 { PIXELATOR_PNA_GRAPH(ch_graph_input) ch_graph = PIXELATOR_PNA_GRAPH.out.pixelfile - ch_versions = ch_versions.mix(PIXELATOR_PNA_GRAPH.out.versions.first()) // // MODULE: Run pixelator single-cell sample-calling @@ -219,8 +205,6 @@ workflow PIXELATOR_PNA_V2 { PIXELATOR_PNA_SAMPLE_CALLING (ch_sample_calling_input) ch_sample_called = PIXELATOR_PNA_SAMPLE_CALLING.out.pixelfile - ch_versions = ch_versions.mix(PIXELATOR_PNA_SAMPLE_CALLING.out.versions.first()) - // Extract the sample names from the pixel file names so that we can // merge them in with the panel file names correctly @@ -242,7 +226,6 @@ workflow PIXELATOR_PNA_V2 { // PIXELATOR_PNA_DENOISE ( ch_sample_called ) ch_denoise = PIXELATOR_PNA_DENOISE.out.pixelfile - ch_versions = ch_versions.mix(PIXELATOR_PNA_DENOISE.out.versions.first()) // // MODULE: Run pixelator single-cell analysis @@ -250,56 +233,38 @@ workflow PIXELATOR_PNA_V2 { ch_analysis_input = params.skip_denoise ? ch_sample_called : ch_denoise PIXELATOR_PNA_ANALYSIS ( ch_analysis_input ) ch_analysis = PIXELATOR_PNA_ANALYSIS.out.pixelfile - ch_versions = ch_versions.mix(PIXELATOR_PNA_ANALYSIS.out.versions.first()) // // MODULE: Run pixelator single-cell layout // PIXELATOR_PNA_LAYOUT( ch_analysis ) - ch_versions = ch_versions.mix(PIXELATOR_PNA_LAYOUT.out.versions.first()) // Prepare all data needed by reporting for each pixelator step ch_input = channel.fromPath(params.input) - ch_all_results_grouped = channel + ch_experiment_summary_input = channel .topic('all_results_for_reports') - .map{ stage, files -> { - tuple(stage, files) - }} - .groupTuple() - - ch_all_results_split_by_stage = ch_all_results_grouped.branch { topic, _files -> - amplicon: topic == 'amplicon' - demux: topic == 'demux' - collapse: topic == 'collapse' - graph: topic == 'graph' - sample_calling: topic == 'sample_calling' - denoise: topic == 'denoise' - analysis: topic == 'analysis' - post_analysis: topic == 'post_analysis' - layout: topic == 'layout' - } - - def pick_file_from_channel = { channel -> - channel.map { _topic, files -> files.flatten() } - } + .map { stage, files -> + def values = files instanceof List ? files : [files] + values.collect { f -> tuple(stage, f) } + } + .flatMap { it } + .collect(flat: false) + .map { stageFilePairs -> + def meta = [id: 'all'] + def stages = stageFilePairs.collect { it[0] } + def files = stageFilePairs.collect { it[1] } + tuple(meta, stages, files) + } if (!params.skip_experiment_summary) { EXPERIMENT_SUMMARY( ch_input, - pick_file_from_channel(ch_all_results_split_by_stage.amplicon), - pick_file_from_channel(ch_all_results_split_by_stage.demux), - pick_file_from_channel(ch_all_results_split_by_stage.collapse), - pick_file_from_channel(ch_all_results_split_by_stage.graph), - pick_file_from_channel(ch_all_results_split_by_stage.sample_calling), - pick_file_from_channel(ch_all_results_split_by_stage.denoise), - pick_file_from_channel(ch_all_results_split_by_stage.analysis), - pick_file_from_channel(ch_all_results_split_by_stage.layout), + ch_experiment_summary_input, ) } emit: - versions = ch_versions graph = ch_graph analysis = ch_analysis } diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 63de15cf..321e5ccd 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -159,10 +159,6 @@ workflow PIPELINE_INITIALISATION { return meta } .join(ch_input) - .map { meta, panel, reads -> - def newMeta = detect_technology(meta) - return [newMeta, panel, reads] - } emit: samplesheet = ch_samplesheet @@ -458,19 +454,3 @@ def validate_input_samplesheet(URI samplesheetUrl, items) { return [meta, panel_file_abs, reads] } - -// -// Inject a `technology` field into the meta map based on the design -// -def detect_technology(LinkedHashMap meta) { - def newMeta = [:] - if (meta.design.startsWith('pna')) { - newMeta = meta + [technology: 'pna'] - } - else { - error("ERROR: unsupported design: ${meta.design}") - } - // TODO For now keep this around, in order to introduce - // other technology choices later. - return newMeta -} diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index 21909ad7..7087a48c 100644 --- a/tests/pna.nf.test.snap +++ b/tests/pna.nf.test.snap @@ -79,7 +79,7 @@ ], { "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.8.6" + "experiment-summary": "0.9.0" }, "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" @@ -124,7 +124,7 @@ 20, { "EXPERIMENT_SUMMARY": { - "experiment-summary": "0.8.6" + "experiment-summary": "0.9.0" }, "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index ffc4aecc..1d3c0e8b 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -63,12 +63,12 @@ workflow PIXELATOR { ch_reads = ch_samplesheet.map { meta, _panel, reads -> [ meta, reads ] } ch_panel_files = ch_samplesheet.map { meta, panel, _reads -> [ meta, panel ] } - if (params.technology == "pna_v1") { + if (params.technology == "proxiome-v1" || params.technology == "nonhashed_samples") { PIXELATOR_PNA_V1( ch_reads, ch_panel_files ) - } else if (params.technology == "pna_v2") { + } else if (params.technology == "proxiome-v2" || params.technology == "hashed_samples") { PIXELATOR_PNA_V2( ch_reads, ch_panel_files From dd8ec658e95461e625272310e3019e633cc06029 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 13 May 2026 14:55:03 +0200 Subject: [PATCH 30/90] Set up tests with synthetic data --- assets/schema_input.json | 10 + conf/base_test.config | 25 ++ ...st_full.config => test_proxiome_v1.config} | 20 +- ...est_pna.config => test_proxiome_v2.config} | 20 +- .../experiment_summary/tests/main.nf.test | 151 +++---- .../tests/main.nf.test.snap | 22 +- modules/local/pixelator/list_options/main.nf | 6 +- .../amplicon/tests/main.nf.test | 12 +- .../amplicon/tests/main.nf.test.snap | 115 ++--- .../analysis/tests/main.nf.test | 8 +- .../analysis/tests/main.nf.test.snap | 143 +++--- .../collapse/tests/main.nf.test | 26 +- .../collapse/tests/main.nf.test.snap | 137 +++--- .../combine_collapse/tests/main.nf.test | 28 +- .../combine_collapse/tests/main.nf.test.snap | 114 ++--- .../single-cell-pna/demux/tests/main.nf.test | 24 +- .../demux/tests/main.nf.test.snap | 199 +++++---- .../denoise/tests/main.nf.test | 8 +- .../denoise/tests/main.nf.test.snap | 142 +++--- .../single-cell-pna/graph/tests/main.nf.test | 12 +- .../graph/tests/main.nf.test.snap | 143 +++--- .../single-cell-pna/layout/tests/main.nf.test | 8 +- .../layout/tests/main.nf.test.snap | 144 +++--- .../sample_calling/tests/main.nf.test | 10 +- .../sample_calling/tests/main.nf.test.snap | 191 ++++---- nextflow.config | 12 +- subworkflows/local/pna/v1/nextflow.config | 7 +- subworkflows/local/pna/v1/tests/main.nf.test | 12 +- .../local/pna/v1/tests/main.nf.test.snap | 137 +++--- subworkflows/local/pna/v2/nextflow.config | 4 + subworkflows/local/pna/v2/tests/main.nf.test | 49 ++ .../local/pna/v2/tests/main.nf.test.snap | 124 ++++++ subworkflows/local/pna/v2/tests/tags.yml | 2 + tests/nextflow.config | 25 +- tests/pna.nf.test.snap | 258 ----------- tests/proxiome_v1.nf.test | 60 +++ tests/proxiome_v1.nf.test.snap | 282 ++++++++++++ tests/{pna.nf.test => proxiome_v2.nf.test} | 17 +- tests/proxiome_v2.nf.test.snap | 418 ++++++++++++++++++ tests/scripts/run_tests_parallel.sh | 15 +- 40 files changed, 1991 insertions(+), 1149 deletions(-) create mode 100644 conf/base_test.config rename conf/{test_full.config => test_proxiome_v1.config} (65%) rename conf/{test_pna.config => test_proxiome_v2.config} (65%) create mode 100644 subworkflows/local/pna/v2/nextflow.config create mode 100644 subworkflows/local/pna/v2/tests/main.nf.test create mode 100644 subworkflows/local/pna/v2/tests/main.nf.test.snap create mode 100644 subworkflows/local/pna/v2/tests/tags.yml delete mode 100644 tests/pna.nf.test.snap create mode 100644 tests/proxiome_v1.nf.test create mode 100644 tests/proxiome_v1.nf.test.snap rename tests/{pna.nf.test => proxiome_v2.nf.test} (66%) create mode 100644 tests/proxiome_v2.nf.test.snap diff --git a/assets/schema_input.json b/assets/schema_input.json index 96d38d3e..f371c18f 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -16,6 +16,16 @@ "description": "Sample name (no spaces).", "meta": ["id"] }, + "pool": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "pool ID cannot contain spaces", + "meta": ["pool"] + }, + "hash_index": { + "type": "integer", + "meta": ["hash_index"] + }, "design": { "type": "string", "pattern": "^\\S+$", diff --git a/conf/base_test.config b/conf/base_test.config new file mode 100644 index 00000000..42cf329b --- /dev/null +++ b/conf/base_test.config @@ -0,0 +1,25 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Base Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Base configuration common to all test profiles +---------------------------------------------------------------------------------------- +*/ + + +// Base directory for nf-core/modules test data +params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pixelator/' + +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } + + // Run a smaller experiment summary for testing + withName: EXPERIMENT_SUMMARY { + ext.args = '-P test_mode="TRUE"' + } +} diff --git a/conf/test_full.config b/conf/test_proxiome_v1.config similarity index 65% rename from conf/test_full.config rename to conf/test_proxiome_v1.config index e9621480..9a9f6bb0 100644 --- a/conf/test_full.config +++ b/conf/test_proxiome_v1.config @@ -6,32 +6,24 @@ for the pna pipline Use as follows: - nextflow run nf-core/pixelator -profile test_pna, --outdir + nextflow run nf-core/pixelator -profile test_proxiome_v1, --outdir ---------------------------------------------------------------------------------------- */ -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h', - ] - // Run a smaller experiment summary for testing - withName: EXPERIMENT_SUMMARY { - ext.args = '-P test_mode="TRUE"' - } -} +includeConfig 'base_test.config' params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile for proxiome v1 data' config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_pna.csv' + input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' pna_graph_component_size_min_threshold = 100 skip_layout = false + technology = "proxiome-v1" + save_all = true } diff --git a/conf/test_pna.config b/conf/test_proxiome_v2.config similarity index 65% rename from conf/test_pna.config rename to conf/test_proxiome_v2.config index e9621480..2c38b6f3 100644 --- a/conf/test_pna.config +++ b/conf/test_proxiome_v2.config @@ -6,32 +6,24 @@ for the pna pipline Use as follows: - nextflow run nf-core/pixelator -profile test_pna, --outdir + nextflow run nf-core/pixelator -profile test_proxiome_v1, --outdir ---------------------------------------------------------------------------------------- */ -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h', - ] - // Run a smaller experiment summary for testing - withName: EXPERIMENT_SUMMARY { - ext.args = '-P test_mode="TRUE"' - } -} +includeConfig 'base_test.config' params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile for proxiome v2 data' config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_pna.csv' + input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' input_basedir = params.pipelines_testdata_base_path + '/testdata/pna' pna_graph_component_size_min_threshold = 100 skip_layout = false + technology = "proxiome-v2" + save_all = true } diff --git a/modules/local/experiment_summary/tests/main.nf.test b/modules/local/experiment_summary/tests/main.nf.test index 55761e46..56bed6aa 100644 --- a/modules/local/experiment_summary/tests/main.nf.test +++ b/modules/local/experiment_summary/tests/main.nf.test @@ -17,49 +17,15 @@ nextflow_process { when { process { """ - input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna.csv', checkIfExists: true) ] + input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] input[1] = [ - [id:'all', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - 'amplicon', 'amplicon', 'amplicon', 'amplicon', - 'demux', 'demux', 'demux', 'demux', - 'collapse', 'collapse', 'collapse', 'collapse', - 'graph', 'graph', 'graph', 'graph', - 'denoise', 'denoise', 'denoise', 'denoise', - 'analysis', 'analysis', 'analysis', 'analysis', - 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', + 'amplicon', 'amplicon', ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.report.json', checkIfExists: true), ] ] """ @@ -87,49 +53,84 @@ nextflow_process { } process { """ - input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna.csv', checkIfExists: true) ] + input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ] input[1] = [ - [id:'all', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ 'amplicon', 'amplicon', 'amplicon', 'amplicon', 'demux', 'demux', 'demux', 'demux', 'collapse', 'collapse', 'collapse', 'collapse', - 'graph', 'graph', 'graph', 'graph', - 'denoise', 'denoise', 'denoise', 'denoise', - 'analysis', 'analysis', 'analysis', 'analysis', - 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', + 'graph', 'graph', 'graph', 'graph', 'graph', 'graph', + 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', 'denoise', + 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', 'analysis', + 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', 'layout', + 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', 'sample_calling', ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.layout.pxl', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool2.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.layout.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/sample4.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1.sample_calling.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1_undetermined.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool1_undetermined.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2.sample_calling.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2_undetermined.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/pool2_undetermined.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample2.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample3.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.dehashed.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.meta.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample4.report.json', checkIfExists: true), ] ] """ diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 4dd334b6..81557181 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -10,15 +10,15 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.9.0 " + "0.10.1 " ] ] ], + "timestamp": "2026-05-13T13:53:08.409767489", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:00:23.063912644" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA experiment summary - stub": { "content": [ @@ -26,14 +26,14 @@ [ "EXPERIMENT_SUMMARY", "experiment-summary", - "0.9.0 " + "0.10.1 " ] ] ], + "timestamp": "2026-05-13T13:50:43.046443239", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T13:57:21.610883862" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } -} +} \ No newline at end of file diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf index 9ed92e48..bef8d5a3 100644 --- a/modules/local/pixelator/list_options/main.nf +++ b/modules/local/pixelator/list_options/main.nf @@ -28,11 +28,13 @@ process PIXELATOR_LIST_OPTIONS { stub: """ cat <<-END_DESIGN > design_options.txt - pna-2 + proxiome-v1 + proxiome-v2 END_DESIGN cat <<-END_PANELS > panel_options.txt - proxiome-immuno-155-v2 + proxiome-v1-immuno-155-v1.1 + proxiome-v2-immuno-155-v1.0 END_PANELS """ } diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test index 3247210a..84ea5a50 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test @@ -16,10 +16,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R1_001.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R2_001.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) ] ] """ @@ -42,10 +42,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R1_001.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R2_001.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) ] ] """ diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap index 8022e139..8f546137 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap @@ -5,48 +5,58 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ + [ + "amplicon", + [ + "pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "5": [ [ "PIXELATOR_PNA_AMPLICON", "pixelator", @@ -56,45 +66,45 @@ "amplicon": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -106,11 +116,11 @@ ] } ], + "timestamp": "2026-05-12T16:46:59.439000448", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T13:57:19.517355298" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA amplicon - small test": { "content": [ @@ -118,11 +128,12 @@ [ "pixelator", "pixelator/amplicon", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.report.json", + "pixelator/amplicon/pool1.amplicon.fq.zst", + "pixelator/amplicon/pool1.meta.json", + "pixelator/amplicon/pool1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-amplicon.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-amplicon.log" ], [ [ @@ -132,10 +143,10 @@ ] ] ], + "timestamp": "2026-05-13T13:51:12.753868531", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T13:58:10.802280883" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test index a17440e7..bcdad4cd 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test @@ -16,8 +16,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } @@ -39,8 +39,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap index 1836f23a..1e1eb10b 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap @@ -5,11 +5,12 @@ [ "pixelator", "pixelator/analysis", - "pixelator/analysis/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/analysis/PNA055_Sample07_filtered_S7.report.json", + "pixelator/analysis/sample1.analysis.pxl", + "pixelator/analysis/sample1.meta.json", + "pixelator/analysis/sample1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-analysis.log" + "pixelator/logs/sample1", + "pixelator/logs/sample1/sample1.pixelator-analysis.log" ], [ [ @@ -19,11 +20,11 @@ ] ] ], + "timestamp": "2026-05-13T13:52:16.675506153", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:01:56.742281294" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA analysis - stub": { "content": [ @@ -31,63 +32,73 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ + [ + "analysis", + [ + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "6": [ [ "PIXELATOR_PNA_ANALYSIS", "pixelator", @@ -97,60 +108,60 @@ "all_results": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-analysis.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -162,10 +173,10 @@ ] } ], + "timestamp": "2026-05-13T08:18:16.640765919", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T13:58:25.311094417" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test index 0ffa619e..3f2d8183 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test @@ -16,13 +16,13 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-immuno-155-v2', // panel - 'pna-2' // design + 'proxiome-v2-immuno-155-v1.0', // panel + 'proxiome-v2' // design ] """ } @@ -44,13 +44,13 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-immuno-155-v2', // panel - 'pna-2' // design + 'proxiome-v2-immuno-155-v1.0', // panel + 'proxiome-v2' // design ] """ } @@ -79,14 +79,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.demux.m1.part_001.parquet', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/pool1.demux.m2.part_000.parquet', checkIfExists: true) ], [], // panel_file - 'proxiome-immuno-155-v2', // panel - 'pna-2' // design + 'proxiome-v2-immuno-155-v1.0', // panel + 'proxiome-v2' // design ] """ } diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap index 41433356..dd9ef4fb 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap @@ -5,11 +5,12 @@ [ "pixelator", "pixelator/collapse", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.report.json", + "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_000.parquet", + "pixelator/collapse/pool1.collapse.m1.part_000.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-collapse.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-collapse.log" ], [ [ @@ -19,11 +20,11 @@ ] ] ], + "timestamp": "2026-05-13T13:52:55.793377791", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:02:49.092397636" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA collapse - stub": { "content": [ @@ -31,52 +32,62 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ + [ + "collapse", + [ + "pool1.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m1.part_000.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "5": [ [ "PIXELATOR_PNA_COLLAPSE", "pixelator", @@ -86,48 +97,48 @@ "collapsed": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.pixelator-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -140,11 +151,11 @@ ] } ], + "timestamp": "2026-05-13T08:15:51.65572364", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:02:16.992233383" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA collapse - small test - multiple files": { "content": [ @@ -152,20 +163,22 @@ [ "pixelator", "pixelator/collapse", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.report.json", + "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_000.parquet", + "pixelator/collapse/pool1.collapse.m1.part_000.report.json", + "pixelator/collapse/pool1.collapse.m2.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_000.parquet", + "pixelator/collapse/pool1.collapse.m2.part_000.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-collapse.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-collapse.log" ], null ], + "timestamp": "2026-05-13T13:53:27.172850517", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:03:21.487439646" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test index 00220c34..9be59a29 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test @@ -18,18 +18,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.report.json', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) ] ] """ @@ -53,18 +49,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.parquet', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.parquet', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.parquet', checkIfExists: true), ], [ - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.report.json', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.report.json', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m1.part_000.report.json', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.m2.part_000.report.json', checkIfExists: true) ] ] """ diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap index 2d7047ad..46af2f92 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap @@ -5,11 +5,11 @@ [ "pixelator", "pixelator/collapse", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.parquet", - "pixelator/collapse/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.report.json", + "pixelator/collapse/pool1.collapse.parquet", + "pixelator/collapse/pool1.meta.json", + "pixelator/collapse/pool1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log" + "pixelator/logs/pool1.pixelator-combine-collapse.log" ], [ [ @@ -19,11 +19,11 @@ ] ] ], + "timestamp": "2026-05-13T08:16:53.369689781", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:04:05.138304037" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA combine collapse - stub": { "content": [ @@ -31,48 +31,58 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ + [ + "collapse", + [ + "pool1.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "5": [ [ "PIXELATOR_PNA_COMBINE_COLLAPSE", "pixelator", @@ -82,45 +92,45 @@ "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-combine-collapse.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.collapse.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "parquet": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.collapse.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -132,10 +142,10 @@ ] } ], + "timestamp": "2026-05-13T08:16:36.538161388", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:03:40.204931897" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test index bf01b060..d5e3c6ac 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test @@ -19,11 +19,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-immuno-155-v2', - 'pna-2' + 'proxiome-v2-immuno-155-v1.0', + 'proxiome-v2' ] """ } @@ -45,11 +45,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-immuno-155-v2', - 'pna-2' + 'proxiome-v2-immuno-155-v1.0', + 'proxiome-v2' ] """ } @@ -80,11 +80,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.amplicon.fq.zst', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/pool1.amplicon.fq.zst', checkIfExists: true), [], - 'proxiome-immuno-155-v2', - 'pna-2' + 'proxiome-v2-immuno-155-v1.0', + 'proxiome-v2' ] """ } diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap index 3b667dcc..106f4bae 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap @@ -5,11 +5,15 @@ [ "pixelator", "pixelator/demux", - "pixelator/demux/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/demux/PNA055_Sample07_filtered_S7.report.json", + "pixelator/demux/pool1.demux.failed.fq.zst", + "pixelator/demux/pool1.demux.m1.part_000.parquet", + "pixelator/demux/pool1.demux.m2.part_000.parquet", + "pixelator/demux/pool1.demux.passed.fq.zst", + "pixelator/demux/pool1.meta.json", + "pixelator/demux/pool1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-demux.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-demux.log" ], [ [ @@ -19,11 +23,11 @@ ] ] ], + "timestamp": "2026-05-13T13:54:49.604614166", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:05:08.373454769" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA demux - stub": { "content": [ @@ -31,73 +35,86 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.demux.m2.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m2.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ + [ + "demux", + [ + "pool1.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m2.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "7": [ [ "PIXELATOR_PNA_DEMUX", "pixelator", @@ -107,70 +124,70 @@ "demuxed": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.demux.m2.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.m1.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.demux.m2.part_000.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "failed": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.failed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-demux.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "passed": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.demux.passed.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -182,11 +199,11 @@ ] } ], + "timestamp": "2026-05-13T08:14:52.528292928", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:04:18.304195722" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA demux - multiple chunks": { "content": [ @@ -194,11 +211,29 @@ [ "pixelator", "pixelator/demux", - "pixelator/demux/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/demux/PNA055_Sample07_filtered_S7.report.json", + "pixelator/demux/pool1.demux.failed.fq.zst", + "pixelator/demux/pool1.demux.m1.part_000.parquet", + "pixelator/demux/pool1.demux.m1.part_001.parquet", + "pixelator/demux/pool1.demux.m1.part_002.parquet", + "pixelator/demux/pool1.demux.m1.part_003.parquet", + "pixelator/demux/pool1.demux.m1.part_004.parquet", + "pixelator/demux/pool1.demux.m1.part_005.parquet", + "pixelator/demux/pool1.demux.m1.part_006.parquet", + "pixelator/demux/pool1.demux.m1.part_007.parquet", + "pixelator/demux/pool1.demux.m2.part_000.parquet", + "pixelator/demux/pool1.demux.m2.part_001.parquet", + "pixelator/demux/pool1.demux.m2.part_002.parquet", + "pixelator/demux/pool1.demux.m2.part_003.parquet", + "pixelator/demux/pool1.demux.m2.part_004.parquet", + "pixelator/demux/pool1.demux.m2.part_005.parquet", + "pixelator/demux/pool1.demux.m2.part_006.parquet", + "pixelator/demux/pool1.demux.m2.part_007.parquet", + "pixelator/demux/pool1.demux.passed.fq.zst", + "pixelator/demux/pool1.meta.json", + "pixelator/demux/pool1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-demux.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-demux.log" ], [ [ @@ -208,10 +243,10 @@ ] ] ], + "timestamp": "2026-05-13T13:55:28.928009264", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:05:49.98769129" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test index 797968f7..fd5eb381 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } @@ -38,8 +38,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/sample_calling/sample1.dehashed.pxl', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap index d6ed52c1..a3e5d7bf 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap @@ -5,11 +5,11 @@ [ "pixelator", "pixelator/denoise", - "pixelator/denoise/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/denoise/PNA055_Sample07_filtered_S7.report.json", + "pixelator/denoise/sample1.meta.json", + "pixelator/denoise/sample1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log" + "pixelator/logs/sample1", + "pixelator/logs/sample1/sample1.pixelator-denoise.log" ], [ [ @@ -19,11 +19,11 @@ ] ] ], + "timestamp": "2026-05-13T08:18:06.55044623", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:20.982865336" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA denoise - stub": { "content": [ @@ -31,63 +31,73 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ + [ + "denoise", + [ + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "6": [ [ "PIXELATOR_PNA_DENOISE", "pixelator", @@ -97,60 +107,60 @@ "all_results": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -162,10 +172,10 @@ ] } ], + "timestamp": "2026-05-13T08:17:51.870638966", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:01.113423824" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test index d71d5032..ab8f7e5f 100644 --- a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test @@ -20,10 +20,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.parquet', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), [], - 'proxiome-immuno-155-v2', + 'proxiome-v2-immuno-155-v1.0', ] """ } @@ -47,10 +47,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.collapse.parquet', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/pool1.collapse.parquet', checkIfExists: true), [], - 'proxiome-immuno-155-v2', + 'proxiome-v2-immuno-155-v1.0', ] """ } diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap index 50b27333..bf1fee4f 100644 --- a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap @@ -5,63 +5,73 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ + [ + "graph", + [ + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "6": [ [ "PIXELATOR_PNA_GRAPH", "pixelator", @@ -71,60 +81,60 @@ "all_results": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-graph.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -136,11 +146,11 @@ ] } ], + "timestamp": "2026-05-13T08:17:03.182656139", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:31.8229537" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "PNA graph - small test": { "content": [ @@ -148,11 +158,12 @@ [ "pixelator", "pixelator/graph", - "pixelator/graph/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/graph/PNA055_Sample07_filtered_S7.report.json", + "pixelator/graph/pool1.graph.pxl", + "pixelator/graph/pool1.meta.json", + "pixelator/graph/pool1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-graph.log" + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-graph.log" ], [ [ @@ -162,10 +173,10 @@ ] ] ], + "timestamp": "2026-05-13T13:56:21.604809809", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:46.156401007" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test index 2fdc8524..429d45ea 100644 --- a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test @@ -22,8 +22,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design: 'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.analysis.pxl', checkIfExists: true) + [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) ] """ } @@ -48,8 +48,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design: 'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.analysis.pxl', checkIfExists: true) + [ id:'sample1', design: 'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/sample1.analysis.pxl', checkIfExists: true) ] """ } diff --git a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap index 2081e913..78ed74dc 100644 --- a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap @@ -4,13 +4,13 @@ 1, [ "pixelator", - "pixelator/PNA055_Sample07_filtered_S7.layout.pxl", "pixelator/layout", - "pixelator/layout/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/layout/PNA055_Sample07_filtered_S7.report.json", + "pixelator/layout/sample1.meta.json", + "pixelator/layout/sample1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-layout.log" + "pixelator/logs/sample1", + "pixelator/logs/sample1/sample1.pixelator-layout.log", + "pixelator/sample1.layout.pxl" ], [ [ @@ -20,11 +20,11 @@ ] ] ], + "timestamp": "2026-05-13T08:19:06.474778967", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2026-02-04T13:06:34.606588167" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "Test PNA layout - stub": { "content": [ @@ -32,63 +32,73 @@ "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ + [ + "layout", + [ + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "6": [ [ "PIXELATOR_PNA_LAYOUT", "pixelator", @@ -98,60 +108,60 @@ "all_results": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pixelator-layout.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "sample1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_pixelator": [ @@ -163,10 +173,10 @@ ] } ], + "timestamp": "2026-05-13T08:18:51.955991713", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2026-02-04T13:06:03.163681958" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test index 44fa9b2c..8566265e 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test @@ -15,8 +15,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), ] """ } // TODO update test files with intermediary files from hashed run @@ -39,8 +40,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ], - file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true), + [ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ], + file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/pool1.graph.pxl', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), ] """ } diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap index 4044f38a..2e8c32ad 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap @@ -1,171 +1,192 @@ { - "PNA denoise - small test": { + "PNA sample calling - small test": { "content": [ 1, [ "pixelator", - "pixelator/denoise", - "pixelator/denoise/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/denoise/PNA055_Sample07_filtered_S7.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log" + "pixelator/logs/pool1.pixelator-sample-calling.log", + "pixelator/sample_calling", + "pixelator/sample_calling/pool1.sample_calling.report.json", + "pixelator/sample_calling/pool1_undetermined.meta.json", + "pixelator/sample_calling/pool1_undetermined.report.json", + "pixelator/sample_calling/sample1.dehashed.pxl", + "pixelator/sample_calling/sample1.meta.json", + "pixelator/sample_calling/sample1.report.json", + "pixelator/sample_calling/sample2.dehashed.pxl", + "pixelator/sample_calling/sample2.meta.json", + "pixelator/sample_calling/sample2.report.json" ], - [ - [ - "PIXELATOR_PNA_DENOISE", - "pixelator", - "0.23.0" - ] - ] + null ], + "timestamp": "2026-05-13T08:17:41.764674925", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:20.982865336" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, - "PNA denoise - stub": { + "PNA sample calling - stub": { "content": [ { "0": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "1": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "4": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-sample-calling.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ [ - "PIXELATOR_PNA_DENOISE", - "pixelator", - "0.23.0" + "sample_calling", + [ + "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], + "6": [ + "versions.yml:md5,ae6f55a43baabae8e12ad36f7860bdfe" + ], "all_results": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, [ - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], "log": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pixelator-denoise.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.pixelator-sample-calling.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metadata_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "report_json": [ [ { - "id": "PNA055_Sample07_filtered_S7", - "design": "pna-2", - "panel": "proxiome-immuno-155-v2", - "technology": "pna" + "id": "pool1", + "design": "proxiome-v2", + "panel": "proxiome-v2-immuno-155-v1.0", + "technology": "proxiome-v2" }, - "PNA055_Sample07_filtered_S7.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions_pixelator": [ - [ - "PIXELATOR_PNA_DENOISE", - "pixelator", - "0.23.0" - ] + "versions": [ + "versions.yml:md5,ae6f55a43baabae8e12ad36f7860bdfe" ] } ], + "timestamp": "2026-05-13T08:17:28.715660092", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-11T14:06:01.113423824" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 04e6f0ef..a253d21e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,11 +249,19 @@ profiles { } test { - includeConfig 'conf/test_pna.config' + includeConfig 'conf/test_proxiome_v1.config' + } + + test_proxiome_v1 { + includeConfig 'conf/test_proxiome_v1.config' + } + + test_proxiome_v2 { + includeConfig 'conf/test_proxiome_v2.config' } test_full { - includeConfig 'conf/test_full.config' + includeConfig 'conf/test_proxiome_v1.config' } cells_1k { diff --git a/subworkflows/local/pna/v1/nextflow.config b/subworkflows/local/pna/v1/nextflow.config index 5809a048..4122edb2 100644 --- a/subworkflows/local/pna/v1/nextflow.config +++ b/subworkflows/local/pna/v1/nextflow.config @@ -1,3 +1,4 @@ -params { - pna_demux_output_chunk_reads = "30K" -} +includeConfig '../../../../conf/base_test.config' + +params.pna_demux_output_chunk_reads = "30K" +params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index 05275ca3..2b35a380 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -1,15 +1,15 @@ nextflow_workflow { - name "Test Workflow PNA" + name "Test Workflow PIXELATOR_PNA_V1" script "../main.nf" config "../nextflow.config" - workflow "PNA" + workflow "PIXELATOR_PNA_V1" tag "subworkflows" tag "subworkflows_pixelator" tag "pixelator" tag "pixelator/pna" - test("Default parameters [design: pna-2, panel: proxiome-immuno-155-v2]") { + test("Default parameters [design: proxiome-v1, panel: proxiome-v1-immuno-155-v1.1]") { when { params { @@ -20,12 +20,12 @@ nextflow_workflow { workflow { """ - def meta = [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155-v2', technology:'pna' ] + def meta = [ id:'sample1', design:'proxiome-v1', panel:'proxiome-v1-immuno-155-v1.1', technology:'proxiome-v1' ] input[0] = Channel.of([ meta, [ - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R1_001.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/PNA055_Sample07_filtered_S7_R2_001.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/sample1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/sample1_R2.fastq.gz', checkIfExists: true) ] ]) input[1] = Channel.of([meta, []]) diff --git a/subworkflows/local/pna/v1/tests/main.nf.test.snap b/subworkflows/local/pna/v1/tests/main.nf.test.snap index 702308f4..596d83a7 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v1/tests/main.nf.test.snap @@ -1,73 +1,98 @@ { - "Default parameters [design: pna-2, panel: proxiome-immuno-155-v2]": { + "Default parameters [design: proxiome-v1, panel: proxiome-v1-immuno-155-v1.1]": { "content": [ - 21, + 19, [ "pixelator", - "pixelator/PNA055_Sample07_filtered_S7.layout.pxl", "pixelator/amplicon", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.report.json", + "pixelator/amplicon/sample1.amplicon.fq.zst", + "pixelator/amplicon/sample1.meta.json", + "pixelator/amplicon/sample1.report.json", "pixelator/analysis", - "pixelator/analysis/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/analysis/PNA055_Sample07_filtered_S7.report.json", + "pixelator/analysis/sample1.analysis.pxl", + "pixelator/analysis/sample1.meta.json", + "pixelator/analysis/sample1.report.json", "pixelator/collapse", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_001.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_002.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_002.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_003.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_003.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_004.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_004.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_005.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_005.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_006.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m1.part_006.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_001.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_002.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_002.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_003.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_003.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_004.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_004.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_005.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_005.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_006.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.m2.part_006.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.parquet", - "pixelator/collapse/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.report.json", + "pixelator/collapse/sample1.collapse.m1.part_000.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_000.parquet", + "pixelator/collapse/sample1.collapse.m1.part_000.report.json", + "pixelator/collapse/sample1.collapse.m1.part_001.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_001.parquet", + "pixelator/collapse/sample1.collapse.m1.part_001.report.json", + "pixelator/collapse/sample1.collapse.m1.part_002.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_002.parquet", + "pixelator/collapse/sample1.collapse.m1.part_002.report.json", + "pixelator/collapse/sample1.collapse.m1.part_003.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_003.parquet", + "pixelator/collapse/sample1.collapse.m1.part_003.report.json", + "pixelator/collapse/sample1.collapse.m1.part_004.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_004.parquet", + "pixelator/collapse/sample1.collapse.m1.part_004.report.json", + "pixelator/collapse/sample1.collapse.m1.part_005.meta.json", + "pixelator/collapse/sample1.collapse.m1.part_005.parquet", + "pixelator/collapse/sample1.collapse.m1.part_005.report.json", + "pixelator/collapse/sample1.collapse.m2.part_000.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_000.parquet", + "pixelator/collapse/sample1.collapse.m2.part_000.report.json", + "pixelator/collapse/sample1.collapse.m2.part_001.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_001.parquet", + "pixelator/collapse/sample1.collapse.m2.part_001.report.json", + "pixelator/collapse/sample1.collapse.m2.part_002.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_002.parquet", + "pixelator/collapse/sample1.collapse.m2.part_002.report.json", + "pixelator/collapse/sample1.collapse.m2.part_003.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_003.parquet", + "pixelator/collapse/sample1.collapse.m2.part_003.report.json", + "pixelator/collapse/sample1.collapse.m2.part_004.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_004.parquet", + "pixelator/collapse/sample1.collapse.m2.part_004.report.json", + "pixelator/collapse/sample1.collapse.m2.part_005.meta.json", + "pixelator/collapse/sample1.collapse.m2.part_005.parquet", + "pixelator/collapse/sample1.collapse.m2.part_005.report.json", + "pixelator/collapse/sample1.collapse.parquet", + "pixelator/collapse/sample1.meta.json", + "pixelator/collapse/sample1.report.json", "pixelator/demux", - "pixelator/demux/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/demux/PNA055_Sample07_filtered_S7.report.json", + "pixelator/demux/sample1.demux.failed.fq.zst", + "pixelator/demux/sample1.demux.m1.part_000.parquet", + "pixelator/demux/sample1.demux.m1.part_001.parquet", + "pixelator/demux/sample1.demux.m1.part_002.parquet", + "pixelator/demux/sample1.demux.m1.part_003.parquet", + "pixelator/demux/sample1.demux.m1.part_004.parquet", + "pixelator/demux/sample1.demux.m1.part_005.parquet", + "pixelator/demux/sample1.demux.m2.part_000.parquet", + "pixelator/demux/sample1.demux.m2.part_001.parquet", + "pixelator/demux/sample1.demux.m2.part_002.parquet", + "pixelator/demux/sample1.demux.m2.part_003.parquet", + "pixelator/demux/sample1.demux.m2.part_004.parquet", + "pixelator/demux/sample1.demux.m2.part_005.parquet", + "pixelator/demux/sample1.demux.passed.fq.zst", + "pixelator/demux/sample1.meta.json", + "pixelator/demux/sample1.report.json", "pixelator/denoise", - "pixelator/denoise/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/denoise/PNA055_Sample07_filtered_S7.report.json", + "pixelator/denoise/sample1.denoised_graph.pxl", + "pixelator/denoise/sample1.meta.json", + "pixelator/denoise/sample1.report.json", "pixelator/graph", - "pixelator/graph/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/graph/PNA055_Sample07_filtered_S7.report.json", + "pixelator/graph/sample1.graph.pxl", + "pixelator/graph/sample1.meta.json", + "pixelator/graph/sample1.report.json", "pixelator/layout", - "pixelator/layout/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/layout/PNA055_Sample07_filtered_S7.report.json", + "pixelator/layout/sample1.layout.pxl", + "pixelator/layout/sample1.meta.json", + "pixelator/layout/sample1.report.json", "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-amplicon.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-analysis.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-demux.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-graph.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-layout.log" + "pixelator/logs/sample1.pixelator-amplicon.log", + "pixelator/logs/sample1.pixelator-analysis.log", + "pixelator/logs/sample1.pixelator-collapse.log", + "pixelator/logs/sample1.pixelator-combine-collapse.log", + "pixelator/logs/sample1.pixelator-demux.log", + "pixelator/logs/sample1.pixelator-denoise.log", + "pixelator/logs/sample1.pixelator-graph.log", + "pixelator/logs/sample1.pixelator-layout.log" ] ], - "timestamp": "2026-05-06T10:58:35.023171035", + "timestamp": "2026-05-13T09:31:53.768855272", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/local/pna/v2/nextflow.config b/subworkflows/local/pna/v2/nextflow.config new file mode 100644 index 00000000..4122edb2 --- /dev/null +++ b/subworkflows/local/pna/v2/nextflow.config @@ -0,0 +1,4 @@ +includeConfig '../../../../conf/base_test.config' + +params.pna_demux_output_chunk_reads = "30K" +params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test new file mode 100644 index 00000000..cc0dbc8f --- /dev/null +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -0,0 +1,49 @@ +nextflow_workflow { + + name "Test Workflow PIXELATOR_PNA_V2" + script "../main.nf" + config "../nextflow.config" + workflow "PIXELATOR_PNA_V2" + tag "subworkflows" + tag "subworkflows_pixelator" + tag "pixelator" + tag "pixelator/pna" + + test("Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v1.0]") { + when { + + params { + pna_graph_component_size_min_threshold = 100 + skip_experiment_summary = true + outdir = "$outputDir" + } + + workflow { + """ + def meta = [ pool:'pool1', id:'sample1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v1' ] + input[0] = Channel.of([ + meta, + [ + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([meta, []]) + """ + } + } + + then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + ).match() } + ) + } + } +} diff --git a/subworkflows/local/pna/v2/tests/main.nf.test.snap b/subworkflows/local/pna/v2/tests/main.nf.test.snap new file mode 100644 index 00000000..a5547b77 --- /dev/null +++ b/subworkflows/local/pna/v2/tests/main.nf.test.snap @@ -0,0 +1,124 @@ +{ + "Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v1.0]": { + "content": [ + 23, + [ + "pixelator", + "pixelator/amplicon", + "pixelator/amplicon/pool1.amplicon.fq.zst", + "pixelator/amplicon/pool1.meta.json", + "pixelator/amplicon/pool1.report.json", + "pixelator/analysis", + "pixelator/analysis/sample1.analysis.pxl", + "pixelator/analysis/sample1.meta.json", + "pixelator/analysis/sample1.report.json", + "pixelator/analysis/sample2.analysis.pxl", + "pixelator/analysis/sample2.meta.json", + "pixelator/analysis/sample2.report.json", + "pixelator/collapse", + "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_000.parquet", + "pixelator/collapse/pool1.collapse.m1.part_000.report.json", + "pixelator/collapse/pool1.collapse.m1.part_001.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_001.parquet", + "pixelator/collapse/pool1.collapse.m1.part_001.report.json", + "pixelator/collapse/pool1.collapse.m1.part_002.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_002.parquet", + "pixelator/collapse/pool1.collapse.m1.part_002.report.json", + "pixelator/collapse/pool1.collapse.m1.part_003.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_003.parquet", + "pixelator/collapse/pool1.collapse.m1.part_003.report.json", + "pixelator/collapse/pool1.collapse.m1.part_004.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_004.parquet", + "pixelator/collapse/pool1.collapse.m1.part_004.report.json", + "pixelator/collapse/pool1.collapse.m1.part_005.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_005.parquet", + "pixelator/collapse/pool1.collapse.m1.part_005.report.json", + "pixelator/collapse/pool1.collapse.m2.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_000.parquet", + "pixelator/collapse/pool1.collapse.m2.part_000.report.json", + "pixelator/collapse/pool1.collapse.m2.part_001.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_001.parquet", + "pixelator/collapse/pool1.collapse.m2.part_001.report.json", + "pixelator/collapse/pool1.collapse.m2.part_002.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_002.parquet", + "pixelator/collapse/pool1.collapse.m2.part_002.report.json", + "pixelator/collapse/pool1.collapse.m2.part_003.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_003.parquet", + "pixelator/collapse/pool1.collapse.m2.part_003.report.json", + "pixelator/collapse/pool1.collapse.m2.part_004.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_004.parquet", + "pixelator/collapse/pool1.collapse.m2.part_004.report.json", + "pixelator/collapse/pool1.collapse.m2.part_005.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_005.parquet", + "pixelator/collapse/pool1.collapse.m2.part_005.report.json", + "pixelator/collapse/pool1.collapse.parquet", + "pixelator/collapse/pool1.meta.json", + "pixelator/collapse/pool1.report.json", + "pixelator/demux", + "pixelator/demux/pool1.demux.failed.fq.zst", + "pixelator/demux/pool1.demux.m1.part_000.parquet", + "pixelator/demux/pool1.demux.m1.part_001.parquet", + "pixelator/demux/pool1.demux.m1.part_002.parquet", + "pixelator/demux/pool1.demux.m1.part_003.parquet", + "pixelator/demux/pool1.demux.m1.part_004.parquet", + "pixelator/demux/pool1.demux.m1.part_005.parquet", + "pixelator/demux/pool1.demux.m2.part_000.parquet", + "pixelator/demux/pool1.demux.m2.part_001.parquet", + "pixelator/demux/pool1.demux.m2.part_002.parquet", + "pixelator/demux/pool1.demux.m2.part_003.parquet", + "pixelator/demux/pool1.demux.m2.part_004.parquet", + "pixelator/demux/pool1.demux.m2.part_005.parquet", + "pixelator/demux/pool1.demux.passed.fq.zst", + "pixelator/demux/pool1.meta.json", + "pixelator/demux/pool1.report.json", + "pixelator/denoise", + "pixelator/denoise/sample1.denoised_graph.pxl", + "pixelator/denoise/sample1.meta.json", + "pixelator/denoise/sample1.report.json", + "pixelator/denoise/sample2.denoised_graph.pxl", + "pixelator/denoise/sample2.meta.json", + "pixelator/denoise/sample2.report.json", + "pixelator/graph", + "pixelator/graph/pool1.graph.pxl", + "pixelator/graph/pool1.meta.json", + "pixelator/graph/pool1.report.json", + "pixelator/layout", + "pixelator/layout/sample1.layout.pxl", + "pixelator/layout/sample1.meta.json", + "pixelator/layout/sample1.report.json", + "pixelator/layout/sample2.layout.pxl", + "pixelator/layout/sample2.meta.json", + "pixelator/layout/sample2.report.json", + "pixelator/logs", + "pixelator/logs/pool1.pixelator-amplicon.log", + "pixelator/logs/pool1.pixelator-collapse.log", + "pixelator/logs/pool1.pixelator-combine-collapse.log", + "pixelator/logs/pool1.pixelator-demux.log", + "pixelator/logs/pool1.pixelator-graph.log", + "pixelator/logs/pool1.pixelator-sample-calling.log", + "pixelator/logs/sample1.pixelator-analysis.log", + "pixelator/logs/sample1.pixelator-denoise.log", + "pixelator/logs/sample1.pixelator-layout.log", + "pixelator/logs/sample2.pixelator-analysis.log", + "pixelator/logs/sample2.pixelator-denoise.log", + "pixelator/logs/sample2.pixelator-layout.log", + "pixelator/sample_calling", + "pixelator/sample_calling/pool1.sample_calling.report.json", + "pixelator/sample_calling/pool1_undetermined.meta.json", + "pixelator/sample_calling/pool1_undetermined.report.json", + "pixelator/sample_calling/sample1.dehashed.pxl", + "pixelator/sample_calling/sample1.meta.json", + "pixelator/sample_calling/sample1.report.json", + "pixelator/sample_calling/sample2.dehashed.pxl", + "pixelator/sample_calling/sample2.meta.json", + "pixelator/sample_calling/sample2.report.json" + ] + ], + "timestamp": "2026-05-13T14:43:57.33706874", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/pna/v2/tests/tags.yml b/subworkflows/local/pna/v2/tests/tags.yml new file mode 100644 index 00000000..0c395141 --- /dev/null +++ b/subworkflows/local/pna/v2/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/pna: + - subworkflows/local/pna/** diff --git a/tests/nextflow.config b/tests/nextflow.config index c19ddeae..e24c0e94 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,34 +4,19 @@ ======================================================================================== */ +includeConfig '../conf/base_test.config' + aws.client.anonymous = true // fixes S3 access issues on self-hosted runners -params { - // Base directory for nf-core/modules test data - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pixelator/' +params.outdir = 'results' +params.modules_testdata_base_path = params.modules_testdata_base_path +params.pipelines_testdata_base_path = params.pipelines_testdata_base_path - // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows - outdir = 'results' -} validation { ignoreParams = ['modules_testdata_base_path', 'pipelines_testdata_base_path'] } -// Impose sensible resource limits for testing -process { - withName: '.*' { - cpus = 2 - memory = 3.GB - time = 2.h - } - - withName: "EXPERIMENT_SUMMARY" { - ext.args = "-P test_mode=\"TRUE\"" - } -} - // Impose same minimum Nextflow version as the pipeline for testing manifest { nextflowVersion = '!>=23.10.4' diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap deleted file mode 100644 index 7087a48c..00000000 --- a/tests/pna.nf.test.snap +++ /dev/null @@ -1,258 +0,0 @@ -{ - "Params: default - stub": { - "content": [ - 20, - [ - "pipeline_info", - "pipeline_info/nf_core_pixelator_software_versions.yml", - "pipeline_info/samplesheet_pna.csv", - "pixelator", - "pixelator/PNA055_Sample07_filtered_S7.pxl", - "pixelator/PNA055_Sample07_unfiltered_S7.pxl", - "pixelator/amplicon", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.report.json", - "pixelator/amplicon/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/amplicon/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/analysis", - "pixelator/analysis/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/analysis/PNA055_Sample07_filtered_S7.report.json", - "pixelator/analysis/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/analysis/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/collapse", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.collapse.parquet", - "pixelator/collapse/PNA055_Sample07_filtered_S7.demux.m1.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.demux.m1.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.demux.m2.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.demux.m2.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_filtered_S7.report.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.collapse.meta.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.collapse.parquet", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.demux.m1.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.demux.m1.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.demux.m2.part_000.meta.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.demux.m2.part_000.report.json", - "pixelator/collapse/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/demux", - 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"pixelator/layout/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/layout/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.demux.m1.part_000.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.demux.m2.part_000.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-amplicon.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-analysis.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-demux.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-graph.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-layout.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7", - "pixelator/logs/PNA055_Sample07_unfiltered_S7.pixelator-combine-collapse.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.demux.m1.part_000.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.demux.m2.part_000.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-amplicon.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-analysis.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-demux.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-denoise.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-graph.log", - 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"PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_AMPLICON": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_ANALYSIS": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_COLLAPSE": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_COMBINE_COLLAPSE": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_DEMUX": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_DENOISE": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_GRAPH": { - "pixelator": "0.26.0" - }, - "PIXELATOR_PNA_LAYOUT": { - "pixelator": "0.26.0" - }, - "Workflow": { - "nf-core/pixelator": "v3.1.0dev" - } - }, - [ - "pipeline_info", - "pipeline_info/nf_core_pixelator_software_versions.yml", - "pipeline_info/samplesheet_pna.csv", - "pixelator", - "pixelator/PNA055_Sample07_filtered_S7.layout.pxl", - "pixelator/PNA055_Sample07_unfiltered_S7.layout.pxl", - "pixelator/amplicon", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.amplicon.fq.zst", - "pixelator/amplicon/PNA055_Sample07_filtered_S7.meta.json", - 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"pixelator/demux/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/denoise", - "pixelator/denoise/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/denoise/PNA055_Sample07_filtered_S7.report.json", - "pixelator/denoise/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/denoise/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/experiment-summary.html", - "pixelator/graph", - "pixelator/graph/PNA055_Sample07_filtered_S7.graph.pxl", - "pixelator/graph/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/graph/PNA055_Sample07_filtered_S7.report.json", - "pixelator/graph/PNA055_Sample07_unfiltered_S7.graph.pxl", - "pixelator/graph/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/graph/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/layout", - "pixelator/layout/PNA055_Sample07_filtered_S7.meta.json", - "pixelator/layout/PNA055_Sample07_filtered_S7.report.json", - "pixelator/layout/PNA055_Sample07_unfiltered_S7.meta.json", - "pixelator/layout/PNA055_Sample07_unfiltered_S7.report.json", - "pixelator/logs", - "pixelator/logs/PNA055_Sample07_filtered_S7", - "pixelator/logs/PNA055_Sample07_filtered_S7.pixelator-combine-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-amplicon.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-analysis.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-demux.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-denoise.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-graph.log", - "pixelator/logs/PNA055_Sample07_filtered_S7/PNA055_Sample07_filtered_S7.pixelator-layout.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7", - "pixelator/logs/PNA055_Sample07_unfiltered_S7.pixelator-combine-collapse.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-amplicon.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-analysis.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-collapse.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-demux.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-denoise.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-graph.log", - "pixelator/logs/PNA055_Sample07_unfiltered_S7/PNA055_Sample07_unfiltered_S7.pixelator-layout.log" - ] - ], - "timestamp": "2026-05-06T14:19:26.290381771", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - } -} \ No newline at end of file diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test new file mode 100644 index 00000000..626a6ff6 --- /dev/null +++ b/tests/proxiome_v1.nf.test @@ -0,0 +1,60 @@ +nextflow_pipeline { + + name "Test PNA pipeline V1" + script "../main.nf" + config "conf/test_proxiome_v1.config" + + tag "pixelator" + tag "pixelator/pna" + + test("Params: all") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), + // All stable path name, with a relative path + stable_name, + ).match() } + ) + } + } + + test("Params: default - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + } + } + + then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), + ).match() } + ) + } + } +} diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap new file mode 100644 index 00000000..a9f352f1 --- /dev/null +++ b/tests/proxiome_v1.nf.test.snap @@ -0,0 +1,282 @@ +{ + "Params: default - stub": { + "content": [ + 21, + [ + "pipeline_info", + "pipeline_info/nf_core_pixelator_software_versions.yml", + "pipeline_info/samplesheet_proxiome_v1.csv", + "pixelator", + "pixelator/amplicon", + "pixelator/amplicon/sample_1.amplicon.fq.zst", + "pixelator/amplicon/sample_1.meta.json", + "pixelator/amplicon/sample_1.report.json", + "pixelator/amplicon/sample_2.amplicon.fq.zst", + "pixelator/amplicon/sample_2.meta.json", + "pixelator/amplicon/sample_2.report.json", + "pixelator/analysis", + "pixelator/analysis/sample_1.meta.json", + "pixelator/analysis/sample_1.pxl", + "pixelator/analysis/sample_1.report.json", + "pixelator/analysis/sample_2.meta.json", + "pixelator/analysis/sample_2.pxl", + "pixelator/analysis/sample_2.report.json", + "pixelator/collapse", + "pixelator/collapse/sample_1.collapse.meta.json", + "pixelator/collapse/sample_1.collapse.parquet", + "pixelator/collapse/sample_1.demux.m1.part_000.meta.json", + "pixelator/collapse/sample_1.demux.m1.part_000.parquet", + "pixelator/collapse/sample_1.demux.m1.part_000.report.json", + "pixelator/collapse/sample_1.demux.m2.part_000.meta.json", + "pixelator/collapse/sample_1.demux.m2.part_000.parquet", + "pixelator/collapse/sample_1.demux.m2.part_000.report.json", + "pixelator/collapse/sample_1.report.json", + "pixelator/collapse/sample_2.collapse.meta.json", + "pixelator/collapse/sample_2.collapse.parquet", + "pixelator/collapse/sample_2.demux.m1.part_000.meta.json", + "pixelator/collapse/sample_2.demux.m1.part_000.parquet", + "pixelator/collapse/sample_2.demux.m1.part_000.report.json", + "pixelator/collapse/sample_2.demux.m2.part_000.meta.json", + "pixelator/collapse/sample_2.demux.m2.part_000.parquet", + "pixelator/collapse/sample_2.demux.m2.part_000.report.json", + "pixelator/collapse/sample_2.report.json", + "pixelator/demux", + "pixelator/demux/sample_1.demux.failed.fq.zst", + "pixelator/demux/sample_1.demux.m1.part_000.parquet", + "pixelator/demux/sample_1.demux.m2.part_000.parquet", + "pixelator/demux/sample_1.demux.passed.fq.zst", + "pixelator/demux/sample_1.meta.json", + "pixelator/demux/sample_1.report.json", + "pixelator/demux/sample_2.demux.failed.fq.zst", + "pixelator/demux/sample_2.demux.m1.part_000.parquet", + "pixelator/demux/sample_2.demux.m2.part_000.parquet", + "pixelator/demux/sample_2.demux.passed.fq.zst", + "pixelator/demux/sample_2.meta.json", + "pixelator/demux/sample_2.report.json", + "pixelator/denoise", + "pixelator/denoise/sample_1.meta.json", + "pixelator/denoise/sample_1.report.json", + "pixelator/denoise/sample_2.meta.json", + "pixelator/denoise/sample_2.report.json", + "pixelator/experiment-summary.html", + "pixelator/graph", + "pixelator/graph/sample_1.meta.json", + "pixelator/graph/sample_1.pxl", + "pixelator/graph/sample_1.report.json", + "pixelator/graph/sample_2.meta.json", + "pixelator/graph/sample_2.pxl", + "pixelator/graph/sample_2.report.json", + "pixelator/layout", + "pixelator/layout/sample_1.meta.json", + "pixelator/layout/sample_1.report.json", + "pixelator/layout/sample_2.meta.json", + "pixelator/layout/sample_2.report.json", + "pixelator/logs", + "pixelator/logs/sample_1", + "pixelator/logs/sample_1.pixelator-combine-collapse.log", + "pixelator/logs/sample_1/sample_1.demux.m1.part_000.pixelator-collapse.log", + "pixelator/logs/sample_1/sample_1.demux.m2.part_000.pixelator-collapse.log", + "pixelator/logs/sample_1/sample_1.pixelator-amplicon.log", + "pixelator/logs/sample_1/sample_1.pixelator-analysis.log", + "pixelator/logs/sample_1/sample_1.pixelator-demux.log", + "pixelator/logs/sample_1/sample_1.pixelator-denoise.log", + "pixelator/logs/sample_1/sample_1.pixelator-graph.log", + "pixelator/logs/sample_1/sample_1.pixelator-layout.log", + "pixelator/logs/sample_2", + "pixelator/logs/sample_2.pixelator-combine-collapse.log", + "pixelator/logs/sample_2/sample_2.demux.m1.part_000.pixelator-collapse.log", + "pixelator/logs/sample_2/sample_2.demux.m2.part_000.pixelator-collapse.log", + "pixelator/logs/sample_2/sample_2.pixelator-amplicon.log", + "pixelator/logs/sample_2/sample_2.pixelator-analysis.log", + "pixelator/logs/sample_2/sample_2.pixelator-demux.log", + "pixelator/logs/sample_2/sample_2.pixelator-denoise.log", + "pixelator/logs/sample_2/sample_2.pixelator-graph.log", + "pixelator/logs/sample_2/sample_2.pixelator-layout.log", + "pixelator/sample_1.pxl", + "pixelator/sample_2.pxl" + ], + { + "CAT_FASTQ": { + "cat": 9.5 + }, + "EXPERIMENT_SUMMARY": { + "experiment-summary": "0.10.1" + }, + "PIXELATOR_LIST_OPTIONS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_AMPLICON": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_ANALYSIS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DEMUX": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DENOISE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_GRAPH": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_LAYOUT": { + "pixelator": "0.26.0" + }, + "Workflow": { + "nf-core/pixelator": "v3.1.0dev" + } + } + ], + "timestamp": "2026-05-13T14:43:44.938290509", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "Params: all": { + "content": [ + 21, + { + "CAT_FASTQ": { + "cat": 9.5 + }, + "EXPERIMENT_SUMMARY": { + "experiment-summary": "0.10.1" + }, + "PIXELATOR_LIST_OPTIONS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_AMPLICON": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_ANALYSIS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DEMUX": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DENOISE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_GRAPH": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_LAYOUT": { + "pixelator": "0.26.0" + }, + "Workflow": { + "nf-core/pixelator": "v3.1.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pixelator_software_versions.yml", + "pipeline_info/samplesheet_proxiome_v1.csv", + "pixelator", + "pixelator/amplicon", + "pixelator/amplicon/sample_1.amplicon.fq.zst", + "pixelator/amplicon/sample_1.meta.json", + "pixelator/amplicon/sample_1.report.json", + "pixelator/amplicon/sample_2.amplicon.fq.zst", + "pixelator/amplicon/sample_2.meta.json", + "pixelator/amplicon/sample_2.report.json", + "pixelator/analysis", + "pixelator/analysis/sample_1.analysis.pxl", + "pixelator/analysis/sample_1.meta.json", + "pixelator/analysis/sample_1.report.json", + "pixelator/analysis/sample_2.analysis.pxl", + "pixelator/analysis/sample_2.meta.json", + "pixelator/analysis/sample_2.report.json", + "pixelator/collapse", + "pixelator/collapse/sample_1.collapse.m1.part_000.meta.json", + "pixelator/collapse/sample_1.collapse.m1.part_000.parquet", + "pixelator/collapse/sample_1.collapse.m1.part_000.report.json", + "pixelator/collapse/sample_1.collapse.m2.part_000.meta.json", + "pixelator/collapse/sample_1.collapse.m2.part_000.parquet", + "pixelator/collapse/sample_1.collapse.m2.part_000.report.json", + "pixelator/collapse/sample_1.collapse.parquet", + "pixelator/collapse/sample_1.meta.json", + "pixelator/collapse/sample_1.report.json", + "pixelator/collapse/sample_2.collapse.m1.part_000.meta.json", + "pixelator/collapse/sample_2.collapse.m1.part_000.parquet", + "pixelator/collapse/sample_2.collapse.m1.part_000.report.json", + "pixelator/collapse/sample_2.collapse.m2.part_000.meta.json", + "pixelator/collapse/sample_2.collapse.m2.part_000.parquet", + "pixelator/collapse/sample_2.collapse.m2.part_000.report.json", + "pixelator/collapse/sample_2.collapse.parquet", + "pixelator/collapse/sample_2.meta.json", + "pixelator/collapse/sample_2.report.json", + "pixelator/demux", + "pixelator/demux/sample_1.demux.failed.fq.zst", + "pixelator/demux/sample_1.demux.m1.part_000.parquet", + "pixelator/demux/sample_1.demux.m2.part_000.parquet", + "pixelator/demux/sample_1.demux.passed.fq.zst", + "pixelator/demux/sample_1.meta.json", + "pixelator/demux/sample_1.report.json", + "pixelator/demux/sample_2.demux.failed.fq.zst", + "pixelator/demux/sample_2.demux.m1.part_000.parquet", + "pixelator/demux/sample_2.demux.m2.part_000.parquet", + "pixelator/demux/sample_2.demux.passed.fq.zst", + "pixelator/demux/sample_2.meta.json", + "pixelator/demux/sample_2.report.json", + "pixelator/denoise", + "pixelator/denoise/sample_1.meta.json", + "pixelator/denoise/sample_1.report.json", + "pixelator/denoise/sample_2.meta.json", + "pixelator/denoise/sample_2.report.json", + "pixelator/experiment-summary.html", + "pixelator/graph", + "pixelator/graph/sample_1.graph.pxl", + "pixelator/graph/sample_1.meta.json", + "pixelator/graph/sample_1.report.json", + "pixelator/graph/sample_2.graph.pxl", + "pixelator/graph/sample_2.meta.json", + "pixelator/graph/sample_2.report.json", + "pixelator/layout", + "pixelator/layout/sample_1.meta.json", + "pixelator/layout/sample_1.report.json", + "pixelator/layout/sample_2.meta.json", + "pixelator/layout/sample_2.report.json", + "pixelator/logs", + "pixelator/logs/sample_1", + "pixelator/logs/sample_1.pixelator-combine-collapse.log", + "pixelator/logs/sample_1/sample_1.pixelator-amplicon.log", + "pixelator/logs/sample_1/sample_1.pixelator-analysis.log", + "pixelator/logs/sample_1/sample_1.pixelator-collapse.log", + "pixelator/logs/sample_1/sample_1.pixelator-demux.log", + "pixelator/logs/sample_1/sample_1.pixelator-denoise.log", + "pixelator/logs/sample_1/sample_1.pixelator-graph.log", + "pixelator/logs/sample_1/sample_1.pixelator-layout.log", + "pixelator/logs/sample_2", + "pixelator/logs/sample_2.pixelator-combine-collapse.log", + "pixelator/logs/sample_2/sample_2.pixelator-amplicon.log", + "pixelator/logs/sample_2/sample_2.pixelator-analysis.log", + "pixelator/logs/sample_2/sample_2.pixelator-collapse.log", + "pixelator/logs/sample_2/sample_2.pixelator-demux.log", + "pixelator/logs/sample_2/sample_2.pixelator-denoise.log", + "pixelator/logs/sample_2/sample_2.pixelator-graph.log", + "pixelator/logs/sample_2/sample_2.pixelator-layout.log", + "pixelator/sample_1.layout.pxl", + "pixelator/sample_2.layout.pxl" + ] + ], + "timestamp": "2026-05-13T13:55:47.469820915", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/tests/pna.nf.test b/tests/proxiome_v2.nf.test similarity index 66% rename from tests/pna.nf.test rename to tests/proxiome_v2.nf.test index e00fa0f2..30c96541 100644 --- a/tests/pna.nf.test +++ b/tests/proxiome_v2.nf.test @@ -1,7 +1,8 @@ nextflow_pipeline { - name "Test PNA pipeline" + name "Test PNA pipeline V2" script "../main.nf" + config "conf/test_proxiome_v2.config" tag "pixelator" tag "pixelator/pna" @@ -11,16 +12,7 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" - input = "$pipelines_testdata_base_path/samplesheet/pna/samplesheet_pna.csv" - input_basedir = "$pipelines_testdata_base_path/testdata/pna/" outdir = "$outputDir" - - pna_graph_component_size_min_threshold = 100 - skip_experiment_summary = false - save_all = true - technology = "pna_v1" - } } @@ -48,12 +40,7 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" - input = "$pipelines_testdata_base_path/samplesheet/pna/samplesheet_pna.csv" - input_basedir = "$pipelines_testdata_base_path/testdata/pna/" outdir = "$outputDir" - - skip_experiment_summary = false } } diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap new file mode 100644 index 00000000..7ed3eb2d --- /dev/null +++ b/tests/proxiome_v2.nf.test.snap @@ -0,0 +1,418 @@ +{ + "Params: default - stub": { + "content": [ + 41, + [ + "pipeline_info", + "pipeline_info/nf_core_pixelator_software_versions.yml", + 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"PIXELATOR_PNA_COMBINE_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DEMUX": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DENOISE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_GRAPH": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_LAYOUT": { + "pixelator": "0.26.0" + }, + "Workflow": { + "nf-core/pixelator": "v3.1.0dev" + } + } + ], + "timestamp": "2026-05-13T14:48:41.140523599", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "Params: all": { + "content": [ + 29, + { + "CAT_FASTQ": { + "cat": 9.5 + }, + "EXPERIMENT_SUMMARY": { + "experiment-summary": "0.10.1" + }, + "PIXELATOR_LIST_OPTIONS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_AMPLICON": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_ANALYSIS": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DEMUX": { + "pixelator": "0.26.0" + }, + "PIXELATOR_PNA_DENOISE": 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+ "pixelator/analysis/sample3.report.json", + "pixelator/analysis/sample4.analysis.pxl", + "pixelator/analysis/sample4.meta.json", + "pixelator/analysis/sample4.report.json", + "pixelator/collapse", + "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m1.part_000.parquet", + "pixelator/collapse/pool1.collapse.m1.part_000.report.json", + "pixelator/collapse/pool1.collapse.m2.part_000.meta.json", + "pixelator/collapse/pool1.collapse.m2.part_000.parquet", + "pixelator/collapse/pool1.collapse.m2.part_000.report.json", + "pixelator/collapse/pool1.collapse.parquet", + "pixelator/collapse/pool1.meta.json", + "pixelator/collapse/pool1.report.json", + "pixelator/collapse/pool2.collapse.m1.part_000.meta.json", + "pixelator/collapse/pool2.collapse.m1.part_000.parquet", + "pixelator/collapse/pool2.collapse.m1.part_000.report.json", + "pixelator/collapse/pool2.collapse.m2.part_000.meta.json", + "pixelator/collapse/pool2.collapse.m2.part_000.parquet", + "pixelator/collapse/pool2.collapse.m2.part_000.report.json", + "pixelator/collapse/pool2.collapse.parquet", + "pixelator/collapse/pool2.meta.json", + "pixelator/collapse/pool2.report.json", + "pixelator/demux", + "pixelator/demux/pool1.demux.failed.fq.zst", + "pixelator/demux/pool1.demux.m1.part_000.parquet", + "pixelator/demux/pool1.demux.m2.part_000.parquet", + "pixelator/demux/pool1.demux.passed.fq.zst", + "pixelator/demux/pool1.meta.json", + "pixelator/demux/pool1.report.json", + "pixelator/demux/pool2.demux.failed.fq.zst", + "pixelator/demux/pool2.demux.m1.part_000.parquet", + "pixelator/demux/pool2.demux.m2.part_000.parquet", + "pixelator/demux/pool2.demux.passed.fq.zst", + "pixelator/demux/pool2.meta.json", + "pixelator/demux/pool2.report.json", + "pixelator/denoise", + "pixelator/denoise/sample1.meta.json", + "pixelator/denoise/sample1.report.json", + "pixelator/denoise/sample2.meta.json", + "pixelator/denoise/sample2.report.json", + "pixelator/denoise/sample3.meta.json", + "pixelator/denoise/sample3.report.json", + "pixelator/denoise/sample4.meta.json", + "pixelator/denoise/sample4.report.json", + "pixelator/experiment-summary.html", + "pixelator/graph", + "pixelator/graph/pool1.graph.pxl", + "pixelator/graph/pool1.meta.json", + "pixelator/graph/pool1.report.json", + "pixelator/graph/pool2.graph.pxl", + "pixelator/graph/pool2.meta.json", + "pixelator/graph/pool2.report.json", + "pixelator/layout", + "pixelator/layout/sample1.meta.json", + "pixelator/layout/sample1.report.json", + "pixelator/layout/sample2.meta.json", + "pixelator/layout/sample2.report.json", + "pixelator/layout/sample3.meta.json", + "pixelator/layout/sample3.report.json", + "pixelator/layout/sample4.meta.json", + "pixelator/layout/sample4.report.json", + "pixelator/logs", + "pixelator/logs/pool1", + "pixelator/logs/pool1.pixelator-combine-collapse.log", + "pixelator/logs/pool1.pixelator-sample-calling.log", + "pixelator/logs/pool1/pool1.pixelator-amplicon.log", + "pixelator/logs/pool1/pool1.pixelator-collapse.log", + "pixelator/logs/pool1/pool1.pixelator-demux.log", + "pixelator/logs/pool1/pool1.pixelator-graph.log", + "pixelator/logs/pool2", + "pixelator/logs/pool2.pixelator-combine-collapse.log", + "pixelator/logs/pool2.pixelator-sample-calling.log", + "pixelator/logs/pool2/pool2.pixelator-amplicon.log", + "pixelator/logs/pool2/pool2.pixelator-collapse.log", + "pixelator/logs/pool2/pool2.pixelator-demux.log", + "pixelator/logs/pool2/pool2.pixelator-graph.log", + "pixelator/logs/sample1", + "pixelator/logs/sample1/sample1.pixelator-analysis.log", + "pixelator/logs/sample1/sample1.pixelator-denoise.log", + "pixelator/logs/sample1/sample1.pixelator-layout.log", + "pixelator/logs/sample2", + "pixelator/logs/sample2/sample2.pixelator-analysis.log", + "pixelator/logs/sample2/sample2.pixelator-denoise.log", + "pixelator/logs/sample2/sample2.pixelator-layout.log", + "pixelator/logs/sample3", + "pixelator/logs/sample3/sample3.pixelator-analysis.log", + "pixelator/logs/sample3/sample3.pixelator-denoise.log", + "pixelator/logs/sample3/sample3.pixelator-layout.log", + "pixelator/logs/sample4", + "pixelator/logs/sample4/sample4.pixelator-analysis.log", + "pixelator/logs/sample4/sample4.pixelator-denoise.log", + "pixelator/logs/sample4/sample4.pixelator-layout.log", + "pixelator/sample1.layout.pxl", + "pixelator/sample2.layout.pxl", + "pixelator/sample3.layout.pxl", + "pixelator/sample4.layout.pxl", + "pixelator/sample_calling", + "pixelator/sample_calling/pool1.sample_calling.report.json", + "pixelator/sample_calling/pool1_undetermined.meta.json", + "pixelator/sample_calling/pool1_undetermined.report.json", + "pixelator/sample_calling/pool2.sample_calling.report.json", + "pixelator/sample_calling/pool2_undetermined.meta.json", + "pixelator/sample_calling/pool2_undetermined.report.json", + "pixelator/sample_calling/sample1.dehashed.pxl", + "pixelator/sample_calling/sample1.meta.json", + "pixelator/sample_calling/sample1.report.json", + "pixelator/sample_calling/sample2.dehashed.pxl", + "pixelator/sample_calling/sample2.meta.json", + "pixelator/sample_calling/sample2.report.json", + "pixelator/sample_calling/sample3.dehashed.pxl", + "pixelator/sample_calling/sample3.meta.json", + "pixelator/sample_calling/sample3.report.json", + "pixelator/sample_calling/sample4.dehashed.pxl", + "pixelator/sample_calling/sample4.meta.json", + "pixelator/sample_calling/sample4.report.json" + ] + ], + "timestamp": "2026-05-13T14:00:08.095379281", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/tests/scripts/run_tests_parallel.sh b/tests/scripts/run_tests_parallel.sh index f339c774..3353cced 100755 --- a/tests/scripts/run_tests_parallel.sh +++ b/tests/scripts/run_tests_parallel.sh @@ -22,10 +22,16 @@ nf-test test --profile test,docker $ARGS \ &> /tmp/pixelator_subworkflow_tests.txt \ && echo "Completed tests: subworkflows" & -echo Running tests: PNA pipeline... +echo Running tests: PNA pipeline V1... nf-test test --profile test,docker $ARGS \ - tests/pna.nf.test \ - &> /tmp/pixelator_pna_pipeline_tests.txt \ + tests/proxiome_v1.nf.test \ + &> /tmp/pixelator_pna_pipeline_v1_tests.txt \ + && echo "Completed tests: PNA pipeline" & + +echo Running tests: PNA pipeline V2... +nf-test test --profile test,docker $ARGS \ + tests/proxiome_v2.nf.test \ + &> /tmp/pixelator_pna_pipeline_v2_tests.txt \ && echo "Completed tests: PNA pipeline" & wait @@ -33,4 +39,5 @@ wait cat /tmp/pixelator_es_tests.txt \ /tmp/pixelator_pna_modules_tests.txt \ /tmp/pixelator_subworkflow_tests.txt \ - /tmp/pixelator_pna_pipeline_tests.txt \ + /tmp/pixelator_pna_pipeline_v1_tests.txt \ + /tmp/pixelator_pna_pipeline_v2_tests.txt \ From b2fc24539f25c253e668af75281daadcbd16e892 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 13 May 2026 15:22:44 +0200 Subject: [PATCH 31/90] Fix linting errors --- conf/test_full.config | 14 ++++++++ nextflow.config | 6 ++-- nextflow_schema.json | 2 +- ro-crate-metadata.json | 2 +- subworkflows/local/pna/v1/meta.yml | 6 ++-- subworkflows/local/pna/v2/main.nf | 1 - subworkflows/local/pna/v2/meta.yml | 55 ++++++++++++++++++++++++++++++ 7 files changed, 79 insertions(+), 7 deletions(-) create mode 100644 conf/test_full.config create mode 100644 subworkflows/local/pna/v2/meta.yml diff --git a/conf/test_full.config b/conf/test_full.config new file mode 100644 index 00000000..6bfdf1ea --- /dev/null +++ b/conf/test_full.config @@ -0,0 +1,14 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test + for the pna pipline + + Use as follows: + nextflow run nf-core/pixelator -profile test_pna, --outdir + +---------------------------------------------------------------------------------------- +*/ + +includeConfig 'test_proxiome_v1.config' diff --git a/nextflow.config b/nextflow.config index a253d21e..5ce76e23 100644 --- a/nextflow.config +++ b/nextflow.config @@ -34,6 +34,8 @@ params { save_pna_denoise_pixelfile = false save_pna_analysis_pixelfile = false + technology = "proxiome-v1" + // PNA amplicon pna_amplicon_mismatches = 0.1 pna_amplicon_remove_polyg = true @@ -62,7 +64,7 @@ params { pna_graph_min_count = 1 pna_graph_max_refinement_recursion_depth = 3 pna_graph_edge_cycle_verification = true - pna_graph_initial_stage_max_edges_to_remove = null + pna_graph_initial_stage_max_edges_to_remove = 10 pna_graph_refinement_stage_max_edges_to_remove = 10 pna_graph_initial_stage_max_edges_to_remove_relative = null pna_graph_refinement_stage_max_edges_to_remove_relative = null @@ -261,7 +263,7 @@ profiles { } test_full { - includeConfig 'conf/test_proxiome_v1.config' + includeConfig 'conf/test_full.config' } cells_1k { diff --git a/nextflow_schema.json b/nextflow_schema.json index 73b52c16..ae9f3110 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -247,7 +247,7 @@ }, "pna_graph_refinement_stage_max_edges_to_remove": { "type": "integer", - "default": 4, + "default": 10, "minimum": 1, "description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery." }, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index c3214f66..2ad49e4a 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-05-06T06:55:20+00:00", - "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details):\n\n`samplesheet.csv`:\n\n```csv\nsample,sample_alias,condition,design,panel,fastq_1,fastq_2\nsample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", + "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details):\n\n`samplesheet.csv`:\n\n```csv\nsample,sample_alias,condition,design,panel,fastq_1,fastq_2\nsample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { "@id": "main.nf" diff --git a/subworkflows/local/pna/v1/meta.yml b/subworkflows/local/pna/v1/meta.yml index 6d581234..ed407abf 100644 --- a/subworkflows/local/pna/v1/meta.yml +++ b/subworkflows/local/pna/v1/meta.yml @@ -1,12 +1,13 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: pna -description: Run the Pixelator single-cell PNA workflow from FASTQ input through graph and analysis outputs. +name: pixelator_pna_v1 +description: Run the Pixelator single-cell PNA proxiome v1 workflow from FASTQ input through graph and analysis outputs. keywords: - pixelator - pna - single-cell - fastq components: + - cat/fastq - pixelator/pna/amplicon - pixelator/pna/demux - pixelator/pna/collapse @@ -15,6 +16,7 @@ components: - pixelator/pna/denoise - pixelator/pna/analysis - pixelator/pna/layout + - experiment/summary - pna_generate_reports input: - fastq: diff --git a/subworkflows/local/pna/v2/main.nf b/subworkflows/local/pna/v2/main.nf index f5417ba2..3f7a9de8 100644 --- a/subworkflows/local/pna/v2/main.nf +++ b/subworkflows/local/pna/v2/main.nf @@ -3,7 +3,6 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { softwareVersionsToYAML } from '../../../nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/pna/v2/meta.yml b/subworkflows/local/pna/v2/meta.yml new file mode 100644 index 00000000..05b0c203 --- /dev/null +++ b/subworkflows/local/pna/v2/meta.yml @@ -0,0 +1,55 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: pixelator_pna_v2 +description: Run the Pixelator single-cell PNA proxiome v2 workflow from FASTQ input through graph and analysis outputs. +keywords: + - pixelator + - pna + - single-cell + - fastq +components: + - cat/fastq + - pixelator/pna/amplicon + - pixelator/pna/demux + - pixelator/pna/collapse + - pixelator/pna/combine/collapse + - pixelator/pna/graph + - pixelator/pna/sample/calling + - pixelator/pna/denoise + - pixelator/pna/analysis + - pixelator/pna/layout + - experiment/summary + - pna_generate_reports +input: + - fastq: + type: file + description: | + Input channel containing sample metadata and one or more FASTQ files. + Structure: [ val(meta), path(reads) ] + pattern: "*.{fq,fastq,fq.gz,fastq.gz,fq.zst,fastq.zst}" + - panel_files: + type: file + description: | + Input channel containing sample metadata and optional panel definition files. + Structure: [ val(meta), path(panel_file) ] + pattern: "*" +output: + - graph: + type: file + description: | + Channel containing graph-stage pixel files. + Structure: [ val(meta), path("*.pxl") ] + pattern: "*.pxl" + - analysis: + type: file + description: | + Channel containing analysis-stage pixel files. + Structure: [ val(meta), path("*.pxl") ] + pattern: "*.pxl" +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" From 2bc9d9e3d1a1f079a14f8e2e572d1b9eb5734347 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 13 May 2026 15:38:35 +0200 Subject: [PATCH 32/90] Update changelog --- CHANGELOG.md | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e5754ab9..4bf66f68 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,29 +5,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev - xxxx-xx-xx +### Added + +- Proxiome V2 workflow by @Aratz [#204](https://github.com/nf-core/pixelator/pull/204) + ### Enhancements & fixes - Use nextflow strict syntax by @Aratz [#194](https://github.com/nf-core/pixelator/pull/194) - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) -- Updated pixelatorES to 0.6.0 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197) +- Updated pixelatorES to 0.10.1 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197), [#204](https://github.com/nf-core/pixelator/pull/204) - Add `cells_1k` and `cells_8k` Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg [#202](https://github.com/nf-core/pixelator/pull/202) ### Software dependencies | Dependency | Old version | New version | | ------------- | ----------- | ----------- | -| `pixelatorES` | 0.6.0 | 0.9.0 | +| `pixelatorES` | 0.6.0 | 0.10.1 | | `pixelatorES` | 0.23.0 | 0.26.0 | ### Parameters -| Old parameter | New parameter | -| ---------------------------------------- | -------------------------------- | -| `--leiden-iterations` | | -| `--min-component-size-in-refinement` | | -| `--min-component-size-to-prune` | | -| | `--edge_cycle-verification` | +| Old parameter | New parameter | +| ------------------------------------ | --------------------------- | +| `--leiden-iterations` | | +| `--min-component-size-in-refinement` | | +| `--min-component-size-to-prune` | | +| | `--edge_cycle-verification` | > [!NOTE] > Parameter has been **updated** if both old and new parameter information is present. From 525727dc8d45b92280b1dcee4e3b4a591e37819e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 13 May 2026 15:50:00 +0200 Subject: [PATCH 33/90] Remove todos --- .../single-cell-pna/sample_calling/tests/main.nf.test | 3 +-- subworkflows/local/pna/v1/main.nf | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test index 8566265e..9dba1c11 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test @@ -20,8 +20,7 @@ nextflow_process { file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true), ] """ - } // TODO update test files with intermediary files from hashed run - // Need hashing panels + } } then { diff --git a/subworkflows/local/pna/v1/main.nf b/subworkflows/local/pna/v1/main.nf index 10a00ea1..24a390d7 100644 --- a/subworkflows/local/pna/v1/main.nf +++ b/subworkflows/local/pna/v1/main.nf @@ -49,7 +49,7 @@ include { CAT_FASTQ } from '../../../../modules/nf-core/cat/ // -workflow PIXELATOR_PNA_V1 { // TODO rename PNA_v1 and move files +workflow PIXELATOR_PNA_V1 { take: ch_fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] ch_panel_files // channel: [ meta, path(panel_file) | ] From 8b7b0c6fa49524b3e61aca4a718f76c66995572b Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 08:53:09 +0200 Subject: [PATCH 34/90] Improve samplesheet validation --- assets/schema_input.json | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/assets/schema_input.json b/assets/schema_input.json index f371c18f..89cd76f5 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -8,6 +8,23 @@ "type": "object", "required": ["sample", "design", "fastq_1"], "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "design": { + "const": "proxiome-v1" + } + } + }, + "then": { + "not": { + "required": ["pool"] + }, + "errorMessage": "Pooled samples can only be used with the `proxiome-v2` design." + } + } + ], "properties": { "sample": { "type": "string", From eba5d7d652919532ce5d08c023d2ef6192df435f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 09:20:53 +0200 Subject: [PATCH 35/90] Update asset samplesheets --- assets/samplesheet_mpx.csv | 4 ---- assets/samplesheet_pna.csv | 3 --- assets/samplesheet_proxiome_v1.csv | 3 +++ assets/samplesheet_proxiome_v2.csv | 3 +++ assets/test_samplesheet.csv | 4 ---- docs/usage.md | 5 +++-- 6 files changed, 9 insertions(+), 13 deletions(-) delete mode 100644 assets/samplesheet_mpx.csv delete mode 100644 assets/samplesheet_pna.csv create mode 100644 assets/samplesheet_proxiome_v1.csv create mode 100644 assets/samplesheet_proxiome_v2.csv delete mode 100644 assets/test_samplesheet.csv diff --git a/assets/samplesheet_mpx.csv b/assets/samplesheet_mpx.csv deleted file mode 100644 index e50611a7..00000000 --- a/assets/samplesheet_mpx.csv +++ /dev/null @@ -1,4 +0,0 @@ -sample,design,panel,fastq_1,fastq_2 -uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L001_R1_001.fastq.gz,uropod_control_S1_L001_R2_001.fastq.gz -uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L002_R1_001.fastq.gz,uropod_control_S1_L002_R2_001.fastq.gz -uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L003_R1_001.fastq.gz,uropod_control_S1_L003_R2_001.fastq.gz diff --git a/assets/samplesheet_pna.csv b/assets/samplesheet_pna.csv deleted file mode 100644 index a59dff3d..00000000 --- a/assets/samplesheet_pna.csv +++ /dev/null @@ -1,3 +0,0 @@ -sample,sample_alias,condition,design,panel,fastq_1,fastq_2 -sample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz -sample2,s2,treatment,pna-2,proxiome-immuno-155-v2,sample2_R1_001.fastq.gz,sample2_R2_001.fastq.gz diff --git a/assets/samplesheet_proxiome_v1.csv b/assets/samplesheet_proxiome_v1.csv new file mode 100644 index 00000000..3b4903ec --- /dev/null +++ b/assets/samplesheet_proxiome_v1.csv @@ -0,0 +1,3 @@ +sample,sample_alias,condition,design,panel,fastq_1,fastq_2 +sample1,s1,control,proxiome-v1,proxiome-v1-immuno-155-v1.1,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz +sample2,s2,treatment,proxiome-v1,proxiome-v1-immuno-155-v1.1,sample2_R1_001.fastq.gz,sample2_R2_001.fastq.gz diff --git a/assets/samplesheet_proxiome_v2.csv b/assets/samplesheet_proxiome_v2.csv new file mode 100644 index 00000000..54d579a4 --- /dev/null +++ b/assets/samplesheet_proxiome_v2.csv @@ -0,0 +1,3 @@ +pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz +pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample2_R1_001.fastq.gz,sample2_R2_001.fastq.gz diff --git a/assets/test_samplesheet.csv b/assets/test_samplesheet.csv deleted file mode 100644 index 9ad1694e..00000000 --- a/assets/test_samplesheet.csv +++ /dev/null @@ -1,4 +0,0 @@ -sample,design,panel,panel_file,fastq_1,fastq_2 -uropod_control_1,D21,,UNO_D21.csv,uropod_control_300k_S1_R1_001.part_001.fastq.gz,uropod_control_300k_S1_R2_001.part_001.fastq.gz -uropod_control_1,D21,,UNO_D21.csv,uropod_control_300k_S1_R1_001.part_002.fastq.gz,uropod_control_300k_S1_R2_001.part_002.fastq.gz -uropod_control_2,D21,human-sc-immunology-spatial-proteomics,,uropod_control_300k_S1_R1_001.fastq.gz,uropod_control_300k_S1_R2_001.fastq.gz diff --git a/docs/usage.md b/docs/usage.md index 81eb28cf..f2baceb2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -15,8 +15,9 @@ Use this parameter to specify its location. --input '[path to samplesheet file]' ``` -We provide an example samplesheet for [PNA data](../assets/samplesheet_pna.csv), -that can be used as a template to create your own samplesheet. +We provide an example samplesheets for [Proxiome v1 data](../assets/samplesheet_proxiome_v1.csv) +and [Proxiome v2 data](../assets/samplesheet_proxiome_v2.csv), that can be used as a template to +create your own samplesheet. ### Format From 3a6c2875b38e82f28040c2d56c69c742425d31c2 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 09:56:55 +0200 Subject: [PATCH 36/90] Update usage.md --- docs/usage.md | 44 +++++++++++++++++++++++++++++++++----------- 1 file changed, 33 insertions(+), 11 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index f2baceb2..bff8f6d7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -33,7 +33,7 @@ to match those defined in the table below. > using for your experiment. Using a mismatched panel file will lead to incorrect antibody > assignments and erroneous results. > -> An update list of which panel files correspond to which kit lot versions can be found +> An updated list of which panel files correspond to which kit lot versions can be found > on the [Pixelgen Technologies website](https://www.pixelgen.com/panel-file-for-data-processing/) Below is an example of a simple samplesheet with two samples. @@ -47,24 +47,46 @@ sample2,s2,treatment,pna-2,proxiome-immuno-155-v2,sample2_R1_001.fastq.gz,sample Columns not defined in the table below are ignored by the pipeline but can be useful to add extra information for downstream processing. -| Column | Required | Description | -| ----------------------------------- | ----------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Yes | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `sample_alias` | Yes (Only for PNA runs) | Custom sample alias. Will be used to identify the sample in reports and visualizations. | -| `condition` | Yes (Only for PNA run) | Experimental condition for the sample (e.g. control, treatment). | -| `design` | Yes | The name of the pixelator design configuration. | -| `panel`
    or
    `panel_file` | Yes | Name of the panel to use.
    or
    Path to a CSV file containing a custom panel. | -| `fastq_1` | Yes | Path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | No | Path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Parameter only used if you are running paired-end. | +| Column | Required | Description | +| ----------------------------------- | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `sample` | Yes | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | +| `sample_alias` | Yes | Custom sample alias. Will be used to identify the sample in reports and visualizations. | +| `condition` | Yes | Custom experimental condition for the sample (e.g. control, treatment). Used for reports and visualizations. | +| `design` | Yes | The name of the pixelator design configuration. | +| `panel`
    or
    `panel_file` | Yes | Name of the panel to use.
    or
    Path to a CSV file containing a custom panel. | +| `fastq_1` | Yes | Path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | No | Path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Parameter only used if you are running paired-end. | +| `pool` | Yes (with pooled samples) | Custom pool name. | +| `hash_index` | Yes (with pooled samples) | Index of the hashing antibody used with this sample. | The `panel` and `panel_file` options are mutually exclusive. If both are specified, the pipeline will throw an error. One of them has to be specified. The pipeline will auto-detect whether a sample is single- or paired-end based on if both `fastq_1` and `fastq_2` or only `fastq_1` is present in the samplesheet. +### Pooling samples + +Pooled samples are supported with the Proxiome v2 kit. To process them, include +the `pool` and `hash_index` columns in the samplesheet and use the +`proxiome-v2` design. Hash indices have to match the hashing antibody used for each sample. + +```csv +pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz +pool2,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz +``` + ### Multiple runs of the same sample -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: +When a sample or pool has been re-sequenced (for example, to increase +sequencing depth), use the same `sample` or `pool` identifier across runs. The +pipeline will then concatenate the corresponding FastQ files before downstream +analysis. + +> [!NOTE] +> When combining multiple runs, sample metadata such as alias, condition, design and panel needs to be repeated on all rows. + +Below is an example for the same sample sequenced across 3 lanes: ```csv title="samplesheet.csv" sample,sample_alias,condition,design,panel,fastq_1,fastq_2 From dd02f7e2b8a7031b2a8187ac1db48bf3f7779130 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 10:56:35 +0200 Subject: [PATCH 37/90] Add missing sample calling parameters --- conf/modules.pna.config | 29 +++ .../single-cell-pna/sample_calling/main.nf | 12 +- .../sample_calling/tests/main.nf.test.snap | 67 +++---- nextflow.config | 6 + nextflow_schema.json | 33 ++++ tests/proxiome_v1.nf.test | 4 +- tests/proxiome_v2.nf.test | 4 +- tests/proxiome_v2.nf.test.snap | 176 ++++++------------ 8 files changed, 174 insertions(+), 157 deletions(-) diff --git a/conf/modules.pna.config b/conf/modules.pna.config index 1c9da75a..dd52039d 100644 --- a/conf/modules.pna.config +++ b/conf/modules.pna.config @@ -155,6 +155,35 @@ process { ] } + withName: PIXELATOR_PNA_SAMPLE_CALLING { + ext.args = { + [ + params.pna_sample_calling_remove_incompatible ? "--remove-incompatible" : '', + params.pna_sample_calling_save_undetermined ? "--save-undetermined" : '', + params.pna_sample_calling_confidence_threshold != null ? "--confidence-threshold ${params.pna_sample_calling_confidence_threshold}" : '', + ].join(' ').trim() + } + publishDir = [ + [ + path: { "${params.outdir}/pixelator" }, + mode: params.publish_dir_mode, + pattern: 'sample_calling/*.pxl', + saveAs: { params.save_pna_sample_calling_pixelfile || params.save_all ? it : null }, + ], + [ + path: { "${params.outdir}/pixelator/logs/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: '*.log', + ], + [ + path: { "${params.outdir}/pixelator" }, + mode: params.publish_dir_mode, + pattern: '**/*.{report,meta}.json', + saveAs: { params.save_json || params.save_all ? it : null }, + ], + ] + } + withName: PIXELATOR_PNA_DENOISE { ext.when = { !params.skip_denoise } ext.args = { diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf index 885f4601..06f26cdb 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf +++ b/modules/local/pixelator/single-cell-pna/sample_calling/main.nf @@ -56,12 +56,12 @@ process PIXELATOR_PNA_SAMPLE_CALLING { """ mkdir sample_calling - touch sample_calling/${prefix}.report.json - touch sample_calling/${prefix}.meta.json - touch sample_calling/${prefix}-S1.pxl - touch sample_calling/${prefix}-S2.pxl - touch sample_calling/${prefix}-S3.pxl - touch sample_calling/${prefix}-S4.pxl + touch sample_calling/${prefix}.sample_calling.report.json + touch sample_calling/${prefix}.sample_calling.meta.json + touch sample_calling/sample1.dehashed.pxl + touch sample_calling/sample2.dehashed.pxl + touch sample_calling/sample3.dehashed.pxl + touch sample_calling/sample4.dehashed.pxl touch ${prefix}.pixelator-sample-calling.log cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap index 2e8c32ad..fbf2cef3 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap @@ -5,7 +5,8 @@ [ "pixelator", "pixelator/logs", - "pixelator/logs/pool1.pixelator-sample-calling.log", + "pixelator/logs/pool1", + "pixelator/logs/pool1/pool1.pixelator-sample-calling.log", "pixelator/sample_calling", "pixelator/sample_calling/pool1.sample_calling.report.json", "pixelator/sample_calling/pool1_undetermined.meta.json", @@ -19,7 +20,7 @@ ], null ], - "timestamp": "2026-05-13T08:17:41.764674925", + "timestamp": "2026-05-18T16:07:43.50926016", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,10 +38,10 @@ "technology": "proxiome-v2" }, [ - "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -52,7 +53,7 @@ "panel": "proxiome-v2-immuno-155-v1.0", "technology": "proxiome-v2" }, - "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -63,7 +64,7 @@ "panel": "proxiome-v2-immuno-155-v1.0", "technology": "proxiome-v2" }, - "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ @@ -75,12 +76,12 @@ "technology": "proxiome-v2" }, [ - "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -99,12 +100,12 @@ [ "sample_calling", [ - "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -120,12 +121,12 @@ "technology": "proxiome-v2" }, [ - "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -148,7 +149,7 @@ "panel": "proxiome-v2-immuno-155-v1.0", "technology": "proxiome-v2" }, - "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pixelfile": [ @@ -160,10 +161,10 @@ "technology": "proxiome-v2" }, [ - "pool1-S1.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S2.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S3.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", - "pool1-S4.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" + "sample1.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.dehashed.pxl:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -175,7 +176,7 @@ "panel": "proxiome-v2-immuno-155-v1.0", "technology": "proxiome-v2" }, - "pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "pool1.sample_calling.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -183,7 +184,7 @@ ] } ], - "timestamp": "2026-05-13T08:17:28.715660092", + "timestamp": "2026-05-18T16:07:27.561906124", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/nextflow.config b/nextflow.config index 5ce76e23..ad816c6b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -31,6 +31,7 @@ params { save_pna_demux_failed_reads = false save_pna_collapsed_reads = false save_pna_graph_pixelfile = false + save_pna_sample_calling_pixelfile = false save_pna_denoise_pixelfile = false save_pna_analysis_pixelfile = false @@ -70,6 +71,11 @@ params { pna_graph_refinement_stage_max_edges_to_remove_relative = null pna_graph_component_size_min_threshold = 8000 + // sample-calling options + pna_sample_calling_remove_incompatible = true + pna_sample_calling_save_undetermined = false + pna_sample_calling_confidence_threshold = 0.9 + // PNA denoise pna_denoise_run_one_core_graph_denoising = true pna_denoise_pval_threshold = 0.05 diff --git a/nextflow_schema.json b/nextflow_schema.json index ae9f3110..6b99efda 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -269,6 +269,36 @@ } } }, + "pna_sample_calling_options": { + "title": "Options for pixelator sample-calling command on PNA data with pooled samples.", + "type": "object", + "fa_icon": "fas fa-vial", + "properties": { + "save_pna_sample_calling_pixelfile": { + "type": "boolean", + "description": "Save the PXL dataset after the sample calling stage.", + "help": "By default, the PXL file after sample calling will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete." + }, + "pna_sample_calling_remove_incompatible": { + "type": "boolean", + "description": "Remove antibodies that are incompatible with their component's called sample.", + "default": true + }, + "pna_sample_calling_save_undetermined": { + "type": "boolean", + "description": "Save components that could not be confidently assigned to any sample.", + "default": false + }, + "pna_sample_calling_confidence_threshold": { + "type": "number", + "description": "Confidence threshold for sample calling.", + "help_text": "Components with a sample confidence below this threshold will be considered undetermined.", + "default": 0.9, + "minimum": 0.0, + "maximum": 1.0 + } + } + }, "pna_denoise_options": { "title": "Denoise options", "type": "object", @@ -565,6 +595,9 @@ { "$ref": "#/$defs/pna_graph_options" }, + { + "$ref": "#/$defs/pna_sample_calling_options" + }, { "$ref": "#/$defs/pna_denoise_options" }, diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index 626a6ff6..0e125ad2 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -11,7 +11,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -39,7 +39,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index 30c96541..838776b2 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -12,7 +12,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -40,7 +40,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 7ed3eb2d..1b38466d 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -15,30 +15,18 @@ "pixelator/amplicon/pool2.meta.json", "pixelator/amplicon/pool2.report.json", "pixelator/analysis", - "pixelator/analysis/pool1-S1.pxl.meta.json", - "pixelator/analysis/pool1-S1.pxl.pxl", - "pixelator/analysis/pool1-S1.pxl.report.json", - "pixelator/analysis/pool1-S2.pxl.meta.json", - "pixelator/analysis/pool1-S2.pxl.pxl", - "pixelator/analysis/pool1-S2.pxl.report.json", - "pixelator/analysis/pool1-S3.pxl.meta.json", - "pixelator/analysis/pool1-S3.pxl.pxl", - "pixelator/analysis/pool1-S3.pxl.report.json", - "pixelator/analysis/pool1-S4.pxl.meta.json", - "pixelator/analysis/pool1-S4.pxl.pxl", - "pixelator/analysis/pool1-S4.pxl.report.json", - "pixelator/analysis/pool2-S1.pxl.meta.json", - "pixelator/analysis/pool2-S1.pxl.pxl", - "pixelator/analysis/pool2-S1.pxl.report.json", - "pixelator/analysis/pool2-S2.pxl.meta.json", - "pixelator/analysis/pool2-S2.pxl.pxl", - "pixelator/analysis/pool2-S2.pxl.report.json", - "pixelator/analysis/pool2-S3.pxl.meta.json", - "pixelator/analysis/pool2-S3.pxl.pxl", - "pixelator/analysis/pool2-S3.pxl.report.json", - "pixelator/analysis/pool2-S4.pxl.meta.json", - "pixelator/analysis/pool2-S4.pxl.pxl", - "pixelator/analysis/pool2-S4.pxl.report.json", + "pixelator/analysis/sample1.meta.json", + "pixelator/analysis/sample1.pxl", + "pixelator/analysis/sample1.report.json", + "pixelator/analysis/sample2.meta.json", + "pixelator/analysis/sample2.pxl", + "pixelator/analysis/sample2.report.json", + "pixelator/analysis/sample3.meta.json", + "pixelator/analysis/sample3.pxl", + "pixelator/analysis/sample3.report.json", + "pixelator/analysis/sample4.meta.json", + "pixelator/analysis/sample4.pxl", + "pixelator/analysis/sample4.report.json", "pixelator/collapse", "pixelator/collapse/pool1.collapse.meta.json", "pixelator/collapse/pool1.collapse.parquet", @@ -72,22 +60,14 @@ "pixelator/demux/pool2.meta.json", "pixelator/demux/pool2.report.json", "pixelator/denoise", - "pixelator/denoise/pool1-S1.pxl.meta.json", - "pixelator/denoise/pool1-S1.pxl.report.json", - "pixelator/denoise/pool1-S2.pxl.meta.json", - "pixelator/denoise/pool1-S2.pxl.report.json", - "pixelator/denoise/pool1-S3.pxl.meta.json", - "pixelator/denoise/pool1-S3.pxl.report.json", - "pixelator/denoise/pool1-S4.pxl.meta.json", - "pixelator/denoise/pool1-S4.pxl.report.json", - "pixelator/denoise/pool2-S1.pxl.meta.json", - "pixelator/denoise/pool2-S1.pxl.report.json", - "pixelator/denoise/pool2-S2.pxl.meta.json", - "pixelator/denoise/pool2-S2.pxl.report.json", - "pixelator/denoise/pool2-S3.pxl.meta.json", - "pixelator/denoise/pool2-S3.pxl.report.json", - "pixelator/denoise/pool2-S4.pxl.meta.json", - "pixelator/denoise/pool2-S4.pxl.report.json", + "pixelator/denoise/sample1.meta.json", + "pixelator/denoise/sample1.report.json", + "pixelator/denoise/sample2.meta.json", + "pixelator/denoise/sample2.report.json", + "pixelator/denoise/sample3.meta.json", + "pixelator/denoise/sample3.report.json", + "pixelator/denoise/sample4.meta.json", + "pixelator/denoise/sample4.report.json", "pixelator/experiment-summary.html", "pixelator/graph", "pixelator/graph/pool1.meta.json", @@ -97,92 +77,60 @@ "pixelator/graph/pool2.pxl", "pixelator/graph/pool2.report.json", "pixelator/layout", - "pixelator/layout/pool1-S1.pxl.meta.json", - "pixelator/layout/pool1-S1.pxl.report.json", - "pixelator/layout/pool1-S2.pxl.meta.json", - "pixelator/layout/pool1-S2.pxl.report.json", - "pixelator/layout/pool1-S3.pxl.meta.json", - "pixelator/layout/pool1-S3.pxl.report.json", - "pixelator/layout/pool1-S4.pxl.meta.json", - "pixelator/layout/pool1-S4.pxl.report.json", - "pixelator/layout/pool2-S1.pxl.meta.json", - "pixelator/layout/pool2-S1.pxl.report.json", - "pixelator/layout/pool2-S2.pxl.meta.json", - "pixelator/layout/pool2-S2.pxl.report.json", - "pixelator/layout/pool2-S3.pxl.meta.json", - "pixelator/layout/pool2-S3.pxl.report.json", - "pixelator/layout/pool2-S4.pxl.meta.json", - "pixelator/layout/pool2-S4.pxl.report.json", + "pixelator/layout/sample1.meta.json", + "pixelator/layout/sample1.report.json", + "pixelator/layout/sample2.meta.json", + "pixelator/layout/sample2.report.json", + "pixelator/layout/sample3.meta.json", + "pixelator/layout/sample3.report.json", + "pixelator/layout/sample4.meta.json", + "pixelator/layout/sample4.report.json", "pixelator/logs", "pixelator/logs/pool1", - "pixelator/logs/pool1-S1.pxl", - "pixelator/logs/pool1-S1.pxl/pool1-S1.pxl.pixelator-analysis.log", - "pixelator/logs/pool1-S1.pxl/pool1-S1.pxl.pixelator-denoise.log", - "pixelator/logs/pool1-S1.pxl/pool1-S1.pxl.pixelator-layout.log", - "pixelator/logs/pool1-S2.pxl", - "pixelator/logs/pool1-S2.pxl/pool1-S2.pxl.pixelator-analysis.log", - "pixelator/logs/pool1-S2.pxl/pool1-S2.pxl.pixelator-denoise.log", - "pixelator/logs/pool1-S2.pxl/pool1-S2.pxl.pixelator-layout.log", - "pixelator/logs/pool1-S3.pxl", - "pixelator/logs/pool1-S3.pxl/pool1-S3.pxl.pixelator-analysis.log", - "pixelator/logs/pool1-S3.pxl/pool1-S3.pxl.pixelator-denoise.log", - "pixelator/logs/pool1-S3.pxl/pool1-S3.pxl.pixelator-layout.log", - "pixelator/logs/pool1-S4.pxl", - "pixelator/logs/pool1-S4.pxl/pool1-S4.pxl.pixelator-analysis.log", - "pixelator/logs/pool1-S4.pxl/pool1-S4.pxl.pixelator-denoise.log", - "pixelator/logs/pool1-S4.pxl/pool1-S4.pxl.pixelator-layout.log", "pixelator/logs/pool1.pixelator-combine-collapse.log", - "pixelator/logs/pool1.pixelator-sample-calling.log", "pixelator/logs/pool1/pool1.demux.m1.part_000.pixelator-collapse.log", "pixelator/logs/pool1/pool1.demux.m2.part_000.pixelator-collapse.log", "pixelator/logs/pool1/pool1.pixelator-amplicon.log", "pixelator/logs/pool1/pool1.pixelator-demux.log", "pixelator/logs/pool1/pool1.pixelator-graph.log", + "pixelator/logs/pool1/pool1.pixelator-sample-calling.log", "pixelator/logs/pool2", - "pixelator/logs/pool2-S1.pxl", - "pixelator/logs/pool2-S1.pxl/pool2-S1.pxl.pixelator-analysis.log", - "pixelator/logs/pool2-S1.pxl/pool2-S1.pxl.pixelator-denoise.log", - "pixelator/logs/pool2-S1.pxl/pool2-S1.pxl.pixelator-layout.log", - "pixelator/logs/pool2-S2.pxl", - "pixelator/logs/pool2-S2.pxl/pool2-S2.pxl.pixelator-analysis.log", - "pixelator/logs/pool2-S2.pxl/pool2-S2.pxl.pixelator-denoise.log", - "pixelator/logs/pool2-S2.pxl/pool2-S2.pxl.pixelator-layout.log", - "pixelator/logs/pool2-S3.pxl", - "pixelator/logs/pool2-S3.pxl/pool2-S3.pxl.pixelator-analysis.log", - "pixelator/logs/pool2-S3.pxl/pool2-S3.pxl.pixelator-denoise.log", - "pixelator/logs/pool2-S3.pxl/pool2-S3.pxl.pixelator-layout.log", - "pixelator/logs/pool2-S4.pxl", - "pixelator/logs/pool2-S4.pxl/pool2-S4.pxl.pixelator-analysis.log", - "pixelator/logs/pool2-S4.pxl/pool2-S4.pxl.pixelator-denoise.log", - "pixelator/logs/pool2-S4.pxl/pool2-S4.pxl.pixelator-layout.log", "pixelator/logs/pool2.pixelator-combine-collapse.log", - "pixelator/logs/pool2.pixelator-sample-calling.log", "pixelator/logs/pool2/pool2.demux.m1.part_000.pixelator-collapse.log", "pixelator/logs/pool2/pool2.demux.m2.part_000.pixelator-collapse.log", "pixelator/logs/pool2/pool2.pixelator-amplicon.log", "pixelator/logs/pool2/pool2.pixelator-demux.log", "pixelator/logs/pool2/pool2.pixelator-graph.log", - "pixelator/pool1-S1.pxl.pxl", - "pixelator/pool1-S2.pxl.pxl", - "pixelator/pool1-S3.pxl.pxl", - "pixelator/pool1-S4.pxl.pxl", - "pixelator/pool2-S1.pxl.pxl", - "pixelator/pool2-S2.pxl.pxl", - "pixelator/pool2-S3.pxl.pxl", - "pixelator/pool2-S4.pxl.pxl", + "pixelator/logs/pool2/pool2.pixelator-sample-calling.log", + "pixelator/logs/sample1", + "pixelator/logs/sample1/sample1.pixelator-analysis.log", + "pixelator/logs/sample1/sample1.pixelator-denoise.log", + "pixelator/logs/sample1/sample1.pixelator-layout.log", + "pixelator/logs/sample2", + "pixelator/logs/sample2/sample2.pixelator-analysis.log", + "pixelator/logs/sample2/sample2.pixelator-denoise.log", + "pixelator/logs/sample2/sample2.pixelator-layout.log", + "pixelator/logs/sample3", + "pixelator/logs/sample3/sample3.pixelator-analysis.log", + "pixelator/logs/sample3/sample3.pixelator-denoise.log", + "pixelator/logs/sample3/sample3.pixelator-layout.log", + "pixelator/logs/sample4", + "pixelator/logs/sample4/sample4.pixelator-analysis.log", + "pixelator/logs/sample4/sample4.pixelator-denoise.log", + "pixelator/logs/sample4/sample4.pixelator-layout.log", + "pixelator/sample1.pxl", + "pixelator/sample2.pxl", + "pixelator/sample3.pxl", + "pixelator/sample4.pxl", "pixelator/sample_calling", - "pixelator/sample_calling/pool1-S1.pxl", - "pixelator/sample_calling/pool1-S2.pxl", - "pixelator/sample_calling/pool1-S3.pxl", - "pixelator/sample_calling/pool1-S4.pxl", - "pixelator/sample_calling/pool1.meta.json", - "pixelator/sample_calling/pool1.report.json", - "pixelator/sample_calling/pool2-S1.pxl", - "pixelator/sample_calling/pool2-S2.pxl", - "pixelator/sample_calling/pool2-S3.pxl", - "pixelator/sample_calling/pool2-S4.pxl", - "pixelator/sample_calling/pool2.meta.json", - "pixelator/sample_calling/pool2.report.json" + "pixelator/sample_calling/pool1.sample_calling.meta.json", + "pixelator/sample_calling/pool1.sample_calling.report.json", + "pixelator/sample_calling/pool2.sample_calling.meta.json", + "pixelator/sample_calling/pool2.sample_calling.report.json", + "pixelator/sample_calling/sample1.dehashed.pxl", + "pixelator/sample_calling/sample2.dehashed.pxl", + "pixelator/sample_calling/sample3.dehashed.pxl", + "pixelator/sample_calling/sample4.dehashed.pxl" ], { "CAT_FASTQ": { @@ -223,7 +171,7 @@ } } ], - "timestamp": "2026-05-13T14:48:41.140523599", + "timestamp": "2026-05-18T11:00:46.039585674", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -356,18 +304,18 @@ "pixelator/logs", "pixelator/logs/pool1", "pixelator/logs/pool1.pixelator-combine-collapse.log", - "pixelator/logs/pool1.pixelator-sample-calling.log", "pixelator/logs/pool1/pool1.pixelator-amplicon.log", "pixelator/logs/pool1/pool1.pixelator-collapse.log", "pixelator/logs/pool1/pool1.pixelator-demux.log", "pixelator/logs/pool1/pool1.pixelator-graph.log", + "pixelator/logs/pool1/pool1.pixelator-sample-calling.log", "pixelator/logs/pool2", "pixelator/logs/pool2.pixelator-combine-collapse.log", - "pixelator/logs/pool2.pixelator-sample-calling.log", "pixelator/logs/pool2/pool2.pixelator-amplicon.log", "pixelator/logs/pool2/pool2.pixelator-collapse.log", "pixelator/logs/pool2/pool2.pixelator-demux.log", "pixelator/logs/pool2/pool2.pixelator-graph.log", + "pixelator/logs/pool2/pool2.pixelator-sample-calling.log", "pixelator/logs/sample1", "pixelator/logs/sample1/sample1.pixelator-analysis.log", "pixelator/logs/sample1/sample1.pixelator-denoise.log", @@ -409,7 +357,7 @@ "pixelator/sample_calling/sample4.report.json" ] ], - "timestamp": "2026-05-13T14:00:08.095379281", + "timestamp": "2026-05-18T10:46:41.797306659", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 6c53173ef76d7a0238911960a23dba7656f564e2 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 11:43:46 +0200 Subject: [PATCH 38/90] Document sample calling output --- docs/output.md | 42 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 37 insertions(+), 5 deletions(-) diff --git a/docs/output.md b/docs/output.md index d74ef1c9..5af05092 100644 --- a/docs/output.md +++ b/docs/output.md @@ -19,6 +19,7 @@ The PNA pipeline consists of the following steps: - [Demultiplexing](#demultiplexing) - [Molecule collapsing and error correction](#molecule-collapsing-and-error-correction) - [Graph construction](#graph-construction) +- [Sample Calling](#sample-calling) - [Denoising](#denoising) - [Analysis](#analysis) - [Layout creation](#compute-layouts-for-visualization) @@ -121,7 +122,37 @@ the [pixelator documentation](https://software.pixelgen.com/pixelator/outputs/px -### Denoising +#### Sample Calling + +This step uses the `pixelator single-cell-pna sample-calling` command. It takes +the graph PXL file and the sample sheet as input and assigns each component to +the most likely sample in pooled experiments. + +Components with assignment confidence below the selected threshold are marked +as undetermined and can be saved to a separate output file. The resulting +per-sample dehashed PXL files are then used as input for the denoising step. + +
    +Output files + +- `pixelator` + - `sample_calling` + - `.dehashed.pxl`: The pixel file containing the data associated with each samples. + - `.meta.json`: Command invocation metadata. + - `.report.json`: QC metrics for the sample calling step. + - `_undetermined.dehashed.pxl`: The pixel file containing data that could not be associated with any sample. + - `_undetermined.meta.json`: Command invocation metadata. + - `_undetermined.report.json`: QC metrics for the sample calling step. + + - `logs` + - `.pixelator-sample-calling.log`: pixelator log output. + +
    + +> [!NOTE] +> This step is run only with `--technology proxiome-v2`. + +#### Denoising This step uses the `pixelator single-cell-pna denoise` command. It will try to find differences between the well-connected parts of each component graph and the less well-connected parts of the graph. It will @@ -145,7 +176,7 @@ The denoised graph will be saved as a new PXL file. -### Analysis +#### Analysis This step uses the `pixelator single-cell-pna analysis` command to calculate spatial statistics. @@ -223,15 +254,16 @@ The output from this step will be placed in the output folder root. ### Output directory structure With default parameters, the pixelator pipeline output directory will only include the latest PXL file -generated by the pipeline (with the most "complete" information) and an interactive HTML report per sample. +generated by the pipeline (with the most "complete" information) and an interactive HTML report summarizing the data for all samples. The PXL dataset files can be from either the `graph`, `analysis` or `layout` step. With default parameters, the `.layout.pxl` will be copied to the output directory. -If the `layout` stage is skipped (using `--skip_layout`) the `.analysis.pxl` files will be included and -if the `analysis` stage is skipped (using `--skip_analysis`) the `.graph.pxl` will be copied. Various flags are available to store intermediate files and are described in the input parameter documentation. Alternatively, you can keep all intermediate files using `--save_all`. +> [!WARNING] +> If the `layout` stage is skipped (using `--skip_layout`), use `--save_pna_` to output the latest PXL files. + Below is an example output structure for a pipeline run using the default settings. - `pipeline_info/` From 0b03a940cad23bc58f65f99b0883f43ed8fd2be7 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 13:22:31 +0200 Subject: [PATCH 39/90] Fix include statements --- subworkflows/local/pna/v1/main.nf | 2 +- subworkflows/local/pna/v2/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/pna/v1/main.nf b/subworkflows/local/pna/v1/main.nf index 24a390d7..e7cfde53 100644 --- a/subworkflows/local/pna/v1/main.nf +++ b/subworkflows/local/pna/v1/main.nf @@ -24,7 +24,7 @@ include { PIXELATOR_PNA_DENOISE } from '../../../../modules/local/pixel include { PIXELATOR_PNA_ANALYSIS } from '../../../../modules/local/pixelator/single-cell-pna/analysis/main' include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/combine_collapse/main' include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout/main' -include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main.nf' +include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/pna/v2/main.nf b/subworkflows/local/pna/v2/main.nf index 3f7a9de8..8b56e83a 100644 --- a/subworkflows/local/pna/v2/main.nf +++ b/subworkflows/local/pna/v2/main.nf @@ -27,8 +27,8 @@ include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixel include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout' -include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main.nf' -include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main.nf' +include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main' +include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 2b1f85acf70c268652152c078c82a18a9d16b08c Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 13:31:12 +0200 Subject: [PATCH 40/90] Add sample calling meta.yml --- .../single-cell-pna/sample_calling/meta.yml | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 modules/local/pixelator/single-cell-pna/sample_calling/meta.yml diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/meta.yml b/modules/local/pixelator/single-cell-pna/sample_calling/meta.yml new file mode 100644 index 00000000..1291c50a --- /dev/null +++ b/modules/local/pixelator/single-cell-pna/sample_calling/meta.yml @@ -0,0 +1,104 @@ +name: pixelator_pna_sample_calling +description: Run `pixelator single-cell-pna sample-calling` to split data into sample-level pixel files. +keywords: + - pixelator + - single-cell-pna + - sample-calling + - pxl +tools: + - pixelator: + description: Single-cell sequencing data analysis toolkit from Pixelgen Technologies. + homepage: https://pixelgen.com/ + documentation: https://software.pixelgen.com/pixelator/ + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - data: + type: file + description: Input file for the sample-calling subcommand. + ontologies: [] + - samplesheet: + type: file + description: Samplesheet used to split results into sample-level outputs. + pattern: "*.{csv,tsv,txt}" + ontologies: [] +output: + pixelfile: + - - meta: + type: map + description: Groovy Map containing sample information. + - "sample_calling/*.pxl": + type: file + description: Sample-level Pixelator PXL output file(s). + pattern: "sample_calling/*.pxl" + ontologies: [] + report_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "sample_calling/*.report.json": + type: file + description: Run report in JSON format. + pattern: "sample_calling/*.report.json" + ontologies: [] + metadata_json: + - - meta: + type: map + description: Groovy Map containing sample information. + - "sample_calling/*.meta.json": + type: file + description: Metadata in JSON format. + pattern: "sample_calling/*.meta.json" + ontologies: [] + all_results: + - - meta: + type: map + description: Groovy Map containing sample information. + - "sample_calling/*": + type: directory + description: All files generated in the sample-calling output directory. + pattern: "sample_calling/*" + ontologies: [] + log: + - - meta: + type: map + description: Groovy Map containing sample information. + - "*pixelator-sample-calling.log": + type: file + description: Pixelator sample-calling command log. + pattern: "*pixelator-sample-calling.log" + ontologies: [] + versions_pixelator: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from. + - pixelator: + type: string + description: The tool name. + - pixelator --version 2>/dev/null | sed 's/pixelator, version //g': + type: eval + description: The expression used to obtain the tool version. +authors: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" +maintainers: + - "@Aratz" + - "@johandahlberg" + - "@fbdtemme" From 1c32a0695d6738de657b79148126736b3e260d09 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 15:43:10 +0200 Subject: [PATCH 41/90] Pimp up parameter schema --- nextflow_schema.json | 78 +++++++++++++++++++++++++++++++++++--------- 1 file changed, 63 insertions(+), 15 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 6b99efda..de733369 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -47,7 +47,7 @@ "pna_amplicon_options": { "title": "Amplicon options", "type": "object", - "fa_icon": "fas fa-circle", + "fa_icon": "fas fa-dna", "properties": { "save_pna_amplicon_reads": { "fa_icon": "fas fa-save", @@ -57,30 +57,33 @@ }, "pna_amplicon_mismatches": { "type": "number", + "fa_icon": "fas fa-not-equal", "minimum": 0, "maximum": 0.5, "description": "The number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]", "default": 0.1 }, "pna_amplicon_remove_polyg": { - "fa_icon": "fas g", "description": "Remove PolyG sequences (length of 10 or more)", + "fa_icon": "fas fa-cut", "type": "boolean", "default": true }, "pna_amplicon_quality_cutoff": { - "fa_icon": "fas gauge", "description": "Minimum average quality a read must have. Pass 0 to disable quality filtering.", + "fa_icon": "fas fa-sliders-h", "type": "integer", "default": 20 }, "pna_amplicon_low_complexity_filter": { "type": "boolean", + "fa_icon": "fas fa-filter", "default": true, "description": "Enable filtering of amplicons with low complexity UMI sequences." }, "pna_amplicon_low_complexity_threshold": { "type": "number", + "fa_icon": "fas fa-percentage", "default": 0.8, "minimum": 0.5, "maximum": 1, @@ -88,11 +91,13 @@ }, "pna_amplicon_lbs_filter": { "type": "boolean", + "fa_icon": "fas fa-filter", "default": true, "description": "Enable filtering of amplicons with UMI sequences that show similarity to the LBS sequence." }, "pna_amplicon_lbs_filter_min_overlap": { "type": "integer", + "fa_icon": "fas fa-arrows-alt-h", "default": 8, "minimum": 4, "maximum": 28, @@ -100,6 +105,7 @@ }, "pna_amplicon_lbs_filter_error_rate": { "type": "number", + "fa_icon": "fas fa-percentage", "default": 0.1, "minimum": 0, "maximum": 1, @@ -110,9 +116,10 @@ "pna_demux_options": { "title": "Demux options", "type": "object", + "fa_icon": "fas fa-random", "properties": { "pna_demux_mismatches": { - "fa_icon": "fas not-equal", + "fa_icon": "fas fa-not-equal", "description": "The number of mismatches allowed in marker barcodes.", "type": "integer", "default": 1, @@ -166,9 +173,10 @@ "pna_collapse_options": { "title": "Collapse options", "type": "object", + "fa_icon": "fas fa-compress-alt", "properties": { "pna_collapse_algorithm": { - "fa_icon": "fas code-fork", + "fa_icon": "fas fa-project-diagram", "description": "The algorithm to use for collapsing.", "default": "directional", "enum": ["cluster", "directional"], @@ -176,7 +184,7 @@ "help": "**cluster:** Form networks of connected UMIs (based on hamming distance threshold). Each connected component is a read group. In the above example, all the UMIs are contained in a single connected component and thus there is one read group containing all reads, with ACGT as the `selected` UMI.\n\n**directional (default):** Form networks with edges defined based on hamming distance threshold and node A counts >= (2 * node B counts) - 1. Each connected component is a read group, with the node with the highest counts selected as the top node for the component." }, "pna_collapse_mismatches": { - "fa_icon": "fas not-equal", + "fa_icon": "fas fa-not-equal", "description": "The number of mismatches allowed when collapsing (adjacency)", "type": "integer", "default": 2, @@ -194,19 +202,23 @@ "pna_graph_options": { "title": "Graph options", "type": "object", + "fa_icon": "fas fa-project-diagram", "properties": { "save_pna_graph_pixelfile": { "type": "boolean", + "fa_icon": "fas fa-save", "description": "Save the PXL dataset after the graph stage.", "help": "By default, the PXL file after graph will not be saved to the results directory unless `--skip_analysis` and `--skip_layout` is passed. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete." }, "pna_graph_multiplet_recovery": { "description": "Activate the multiplet recovery using leiden community detection", + "fa_icon": "fas fa-project-diagram", "type": "boolean", "default": true }, "pna_graph_initial_stage_leiden_resolution": { - "default": 1, + "default": 1.0, + "fa_icon": "fas fa-sliders-h", "minimum": 0, "type": "number", "description": "The resolution parameter for the leiden algorithm at the initial stage.", @@ -214,6 +226,7 @@ }, "pna_graph_refinement_stage_leiden_resolution": { "default": 0.01, + "fa_icon": "fas fa-sliders-h", "minimum": 0, "type": "number", "description": "The resolution parameter for the leiden algorithm at the refinement stage.", @@ -221,12 +234,14 @@ }, "pna_graph_edge_cycle_verification": { "type": "boolean", + "fa_icon": "fas fa-check-circle", "default": true, "description": "Activate edge cycle verification to remove edges from well connected regions that are not part of cycles in the graph.", "help": "This option can help improve the quality of the graph by removing potentially false edges." }, "pna_graph_min_count": { - "default": 1, + "default": 1.0, + "fa_icon": "fas fa-hashtag", "maximum": 50, "minimum": 0, "type": "number", @@ -234,6 +249,7 @@ }, "pna_graph_max_refinement_recursion_depth": { "type": "integer", + "fa_icon": "fas fa-sitemap", "default": 3, "minimum": 1, "maximum": 100, @@ -241,28 +257,33 @@ }, "pna_graph_initial_stage_max_edges_to_remove": { "type": "integer", + "fa_icon": "fas fa-trash", "default": 10, "minimum": 1, "description": "The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery." }, "pna_graph_refinement_stage_max_edges_to_remove": { "type": "integer", + "fa_icon": "fas fa-trash", "default": 10, "minimum": 1, "description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery." }, "pna_graph_initial_stage_max_edges_to_remove_relative": { "type": "number", + "fa_icon": "fas fa-trash", "minimum": 0, "description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the initial stage (iteration == 0) of multiplet recovery." }, "pna_graph_refinement_stage_max_edges_to_remove_relative": { "type": "number", + "fa_icon": "fas fa-trash", "minimum": 0, "description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery." }, "pna_graph_component_size_min_threshold": { "type": "integer", + "fa_icon": "fas fa-expand-alt", "minimum": 1, "default": 8000, "description": "Components with fewer nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data." @@ -270,27 +291,31 @@ } }, "pna_sample_calling_options": { - "title": "Options for pixelator sample-calling command on PNA data with pooled samples.", + "title": "Sample calling options", "type": "object", "fa_icon": "fas fa-vial", "properties": { "save_pna_sample_calling_pixelfile": { "type": "boolean", + "fa_icon": "fas fa-save", "description": "Save the PXL dataset after the sample calling stage.", "help": "By default, the PXL file after sample calling will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete." }, - "pna_sample_calling_remove_incompatible": { - "type": "boolean", - "description": "Remove antibodies that are incompatible with their component's called sample.", - "default": true - }, "pna_sample_calling_save_undetermined": { "type": "boolean", + "fa_icon": "fas fa-save", "description": "Save components that could not be confidently assigned to any sample.", "default": false }, + "pna_sample_calling_remove_incompatible": { + "type": "boolean", + "fa_icon": "fas fa-trash", + "description": "Remove antibodies that are incompatible with their component's called sample.", + "default": true + }, "pna_sample_calling_confidence_threshold": { "type": "number", + "fa_icon": "fas fa-percentage", "description": "Confidence threshold for sample calling.", "help_text": "Components with a sample confidence below this threshold will be considered undetermined.", "default": 0.9, @@ -302,9 +327,11 @@ "pna_denoise_options": { "title": "Denoise options", "type": "object", + "fa_icon": "fas fa-microscope", "properties": { "skip_denoise": { "description": "Skip denoise step", + "fa_icon": "fas fa-forward", "type": "boolean" }, "save_pna_denoise_pixelfile": { @@ -315,17 +342,20 @@ }, "pna_denoise_run_one_core_graph_denoising": { "description": "Activate the one-core graph denoising algorithm", + "fa_icon": "fas fa-microscope", "type": "boolean", "default": true }, "pna_denoise_pval_threshold": { "type": "number", + "fa_icon": "fas fa-flask", "description": "The p-value threshold for the a marker to be considered significantly over-expressed in the one-core layer of a component", "default": 0.05, "minimum": 0 }, "pna_denoise_inflate_factor": { "type": "number", + "fa_icon": "fas fa-expand-arrows-alt", "description": "The inflate factor for the number of nodes from over-expressed markers to be removed from the one-core layer of a component", "default": 1.5, "minimum": 1 @@ -335,9 +365,11 @@ "pna_analysis_options": { "title": "Analysis options", "type": "object", + "fa_icon": "fas fa-chart-line", "properties": { "skip_analysis": { "description": "Skip analysis step", + "fa_icon": "fas fa-forward", "type": "boolean" }, "save_pna_analysis_pixelfile": { @@ -348,27 +380,32 @@ }, "pna_analysis_compute_proximity": { "description": "Compute proximity scores", + "fa_icon": "fas fa-ruler-combined", "type": "boolean", "default": true }, "pna_analysis_compute_k_cores": { "description": "Compute k-core summary tables for each component", + "fa_icon": "fas fa-network-wired", "type": "boolean", "default": true }, "pna_analysis_proximity_nbr_of_permutations": { "type": "integer", + "fa_icon": "fas fa-random", "description": "Number of permutations to use when computing the expected proximity scores", "default": 100, "minimum": 50 }, "pna_analysis_compute_svd_var_explained": { "description": "Compute the variance explained by the SVD components", + "fa_icon": "fas fa-chart-pie", "type": "boolean", "default": true }, "pna_analysis_svd_nbr_of_pivots": { "type": "integer", + "fa_icon": "fas fa-compass", "description": "Number of pivots to use for the SVD decomposition", "default": 50, "minimum": 10, @@ -379,29 +416,35 @@ "pna_layout_options": { "title": "Layout options", "type": "object", + "fa_icon": "fas fa-draw-polygon", "properties": { "skip_layout": { "description": "Skip layout step", + "fa_icon": "fas fa-forward", "type": "boolean" }, "pna_layout_no_node_marker_counts": { "description": "Skip adding marker counts to the layout.", + "fa_icon": "fas fa-ban", "type": "boolean" }, "pna_layout_layout_algorithm": { "description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d.", + "fa_icon": "fas fa-project-diagram", "type": "string", "enum": ["pmds_3d", "wpmds_3d"], "default": "wpmds_3d" }, "pna_layout_pmds_pivots": { "type": "integer", + "fa_icon": "fas fa-compass", "description": "Number of pivots to use for the PMDS layout algorithm. Default: 50. More gives better results, but increases computation time.", "default": 50, "minimum": 50 }, "pna_layout_wpmds_k": { "type": "integer", + "fa_icon": "fas fa-ruler", "description": "The window size used when computing probability weights for the wpmds layout method. Only used when layout algorithm is set to wpmds.", "default": 5, "minimum": 1, @@ -412,9 +455,11 @@ "experiment_summary_options": { "title": "Experiment Summary options", "type": "object", + "fa_icon": "fas fa-clipboard-list", "properties": { "skip_experiment_summary": { "description": "Skip experiment summary generation", + "fa_icon": "fas fa-forward", "type": "boolean" } } @@ -422,15 +467,18 @@ "global_config_options": { "title": "Global options", "type": "object", + "fa_icon": "fas fa-cogs", "description": "Global configuration options specific to nf-core/pixelator.", "properties": { "pixelator_container": { "type": "string", + "fa_icon": "fas fa-box", "description": "Override the container image reference to use for all steps using the `pixelator` command.", "help_text": "Use this to force the pipeline to use a different image version in all steps that use the pixelator command.\nThe pipeline is not guaranteed to work when using different pixelator versions." }, "experiment_summary_container": { "type": "string", + "fa_icon": "fas fa-box", "description": "Override the container image to use for the experiment summary step.", "help_text": "Use this to force the pipeline to use a different image version for the experiment summary step.\nThe pipeline is not guaranteed to work when using different experiment summary versions." }, @@ -448,6 +496,7 @@ }, "technology": { "type": "string", + "fa_icon": "fas fa-microchip", "description": "The technology used to process the samples", "enum": ["proxiome-v1", "proxiome-v2", "hashed_samples", "nonhashed_samples"], "default": "proxiome-v1" @@ -560,7 +609,6 @@ }, "trace_report_suffix": { "type": "string", - "fa_icon": "far calendar", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true }, From 0610de54e6e1c9386b7ecc523f0bc68eca0eb608 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 15:47:13 +0200 Subject: [PATCH 42/90] Fix schema warning --- nextflow_schema.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index de733369..5ef3a3c4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -304,8 +304,7 @@ "pna_sample_calling_save_undetermined": { "type": "boolean", "fa_icon": "fas fa-save", - "description": "Save components that could not be confidently assigned to any sample.", - "default": false + "description": "Save components that could not be confidently assigned to any sample." }, "pna_sample_calling_remove_incompatible": { "type": "boolean", From 732083631168d36502110343aefe55c538224277 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 15:51:43 +0200 Subject: [PATCH 43/90] Update metro map Co-authored-by: Max Karlsson --- docs/images/nf-core-pixelator-metromap.svg | 456 ++++++++------------- 1 file changed, 178 insertions(+), 278 deletions(-) diff --git a/docs/images/nf-core-pixelator-metromap.svg b/docs/images/nf-core-pixelator-metromap.svg index 3eb27166..94f5f6f3 100644 --- a/docs/images/nf-core-pixelator-metromap.svg +++ b/docs/images/nf-core-pixelator-metromap.svg @@ -1,373 +1,273 @@ - + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - + + + + + + - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + + + + + + + + + + - - - - - - + + + + + + + + - - - - - - + + + + + - - - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - - - - - - - - - - - - - - - - - - - + - + - - - - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + From 6eb6a5c40bb3292cd74ff0e9c6218faab3a19533 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 16:17:49 +0200 Subject: [PATCH 44/90] Update readme --- README.md | 23 ++++++++++++++++------- ro-crate-metadata.json | 2 +- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a0d5150c..2b39b6ce 100644 --- a/README.md +++ b/README.md @@ -35,15 +35,20 @@ The pipeline will run the following steps: 2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator)) 3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator)) 4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator)) -5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator)) -6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator)) -7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator)) -8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES) +5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator)) + +6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator)) +7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator)) +8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator)) +9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES) > [!NOTE] > If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/), > which is the last version to support that data type. +> [!NOTE] +> TODO panel and design update 4.0 + > [!WARNING] > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. > This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable @@ -54,15 +59,19 @@ The pipeline will run the following steps: > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. -First, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details): +First, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details). +For hashed PNA data (Proxiome kit v2), the samplesheet will look as follows: `samplesheet.csv`: ```csv -sample,sample_alias,condition,design,panel,fastq_1,fastq_2 -sample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz +pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz ``` +> [!NOTE] +> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv) + Each row represents a sample and gives the design, a panel file and the input fastq files. Now, you can run the pipeline using: diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 2ad49e4a..cbab4744 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-05-06T06:55:20+00:00", - "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n6. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details):\n\n`samplesheet.csv`:\n\n```csv\nsample,sample_alias,condition,design,panel,fastq_1,fastq_2\nsample1,s1,control,pna-2,proxiome-immuno-155-v2,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", + "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. *(Conditional; only for PNA hashed data)* Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!NOTE]\n> TODO panel and design update 4.0\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\n>[!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { "@id": "main.nf" From d0ef908461e75d99cb8b40f5ef5fa702c217773f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 18 May 2026 16:23:53 +0200 Subject: [PATCH 45/90] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4bf66f68..22352c2f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- Proxiome V2 workflow by @Aratz [#204](https://github.com/nf-core/pixelator/pull/204) +- Proxiome V2 workflow by @Aratz [#204](https://github.com/nf-core/pixelator/pull/204), [#205](https://github.com/nf-core/pixelator/pull/205) ### Enhancements & fixes From be7a03a10b990ae031b7cbbe31c2aec1ab498ef4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:11:39 +0200 Subject: [PATCH 46/90] Clarify sample calling output Co-authored-by: Johan Dahlberg --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 5af05092..3959f97e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -140,7 +140,7 @@ per-sample dehashed PXL files are then used as input for the denoising step. - `.dehashed.pxl`: The pixel file containing the data associated with each samples. - `.meta.json`: Command invocation metadata. - `.report.json`: QC metrics for the sample calling step. - - `_undetermined.dehashed.pxl`: The pixel file containing data that could not be associated with any sample. + - `_undetermined.dehashed.pxl`: The pixel file containing data that could not be associated with any sample. This is only output when `pna_sample_calling_save_undetermined = true`. - `_undetermined.meta.json`: Command invocation metadata. - `_undetermined.report.json`: QC metrics for the sample calling step. From 34eeef05cca128634d0d9c38ddb97879c61d0062 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:12:14 +0200 Subject: [PATCH 47/90] Improve language Co-authored-by: Johan Dahlberg --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 3959f97e..9ab78fcf 100644 --- a/docs/output.md +++ b/docs/output.md @@ -150,7 +150,7 @@ per-sample dehashed PXL files are then used as input for the denoising step. > [!NOTE] -> This step is run only with `--technology proxiome-v2`. +> This step is run only when `--technology proxiome-v2` is set. #### Denoising From 33884ac0382d8d224d052f633566a0fabe936c86 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:13:42 +0200 Subject: [PATCH 48/90] Reorder samplesheet columns in usage.md Co-authored-by: Johan Dahlberg --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index bff8f6d7..f4fa63de 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -49,6 +49,8 @@ to add extra information for downstream processing. | Column | Required | Description | | ----------------------------------- | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `pool` | Yes (with pooled samples) | Custom pool name. | +| `hash_index` | Yes (with pooled samples) | Index of the hashing antibody used with this sample. | | `sample` | Yes | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | | `sample_alias` | Yes | Custom sample alias. Will be used to identify the sample in reports and visualizations. | | `condition` | Yes | Custom experimental condition for the sample (e.g. control, treatment). Used for reports and visualizations. | @@ -56,8 +58,6 @@ to add extra information for downstream processing. | `panel`
    or
    `panel_file` | Yes | Name of the panel to use.
    or
    Path to a CSV file containing a custom panel. | | `fastq_1` | Yes | Path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | No | Path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Parameter only used if you are running paired-end. | -| `pool` | Yes (with pooled samples) | Custom pool name. | -| `hash_index` | Yes (with pooled samples) | Index of the hashing antibody used with this sample. | The `panel` and `panel_file` options are mutually exclusive. If both are specified, the pipeline will throw an error. One of them has to be specified. From b1e2e1bcfc56d5832e7624409bd758e6dac93293 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:14:34 +0200 Subject: [PATCH 49/90] Specify typical number of hashed samples per pool Co-authored-by: Johan Dahlberg --- docs/usage.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/usage.md b/docs/usage.md index f4fa63de..1c1f2fe7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -69,6 +69,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end based on Pooled samples are supported with the Proxiome v2 kit. To process them, include the `pool` and `hash_index` columns in the samplesheet and use the `proxiome-v2` design. Hash indices have to match the hashing antibody used for each sample. +Typically there are 8 hashed samples per pool (numbering 1 to 8). ```csv pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 From 6157fd5a562400f14a74c8ec8ac6f747170a2e6d Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:15:27 +0200 Subject: [PATCH 50/90] Clarify row repetition Co-authored-by: Johan Dahlberg --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 1c1f2fe7..fa4d2272 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,7 +85,7 @@ pipeline will then concatenate the corresponding FastQ files before downstream analysis. > [!NOTE] -> When combining multiple runs, sample metadata such as alias, condition, design and panel needs to be repeated on all rows. +> When combining multiple runs, sample metadata such as pool, hash_index, sample_alias, condition, design and panel needs to be repeated on all rows. Below is an example for the same sample sequenced across 3 lanes: From e0772c31d0b304ee153548287b923b8acce7b318 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:31:32 +0200 Subject: [PATCH 51/90] Clarify parameter description Co-authored-by: Johan Dahlberg --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5ef3a3c4..a3b6d885 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -304,7 +304,7 @@ "pna_sample_calling_save_undetermined": { "type": "boolean", "fa_icon": "fas fa-save", - "description": "Save components that could not be confidently assigned to any sample." + "description": "Save components that could not be confidently assigned to any sample to a separate pxl file." }, "pna_sample_calling_remove_incompatible": { "type": "boolean", From 96b62ed666632b5720d9caa819f32c5221134b27 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:32:18 +0200 Subject: [PATCH 52/90] Remove extra line in README Co-authored-by: Johan Dahlberg --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 2b39b6ce..4d1c3208 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,6 @@ The pipeline will run the following steps: 3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator)) 4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator)) 5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator)) - 6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator)) 7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator)) 8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator)) From 8516df8287880fbd5984f93ffea61e3f78988816 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:10:54 +0200 Subject: [PATCH 53/90] Improve samplesheet validation --- assets/schema_input.json | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/assets/schema_input.json b/assets/schema_input.json index 89cd76f5..41df445d 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -23,6 +23,23 @@ }, "errorMessage": "Pooled samples can only be used with the `proxiome-v2` design." } + }, + { + "if": { + "properties": { + "design": { + "const": "proxiome-v2" + }, + "panel": { + "const": "proxiome-v2-immuno-155-v1.0" + } + }, + "required": ["design", "panel"] + }, + "then": { + "required": ["pool", "hash_index"], + "errorMessage": "The `pool` and `hash_index` columns are required for `proxiome-v2` design with panel `proxiome-v2-immuno-155-v1.0`." + } } ], "properties": { From 4759896ed731920e7d354d4944330c87ee417a5b Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:30:03 +0200 Subject: [PATCH 54/90] Add example with resequenced pools --- docs/usage.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index fa4d2272..e4a7d4da 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -96,6 +96,16 @@ uropod_control_1,s1,control,pna-2,proxiome-immuno-155-v2,uropod_control_S1_L002_ uropod_control_1,s1,control,pna-2,proxiome-immuno-155-v2,uropod_control_S1_L003_R1_001.fastq.gz,uropod_control_S1_L003_R2_001.fastq.gz ``` +The same approach applies when pooled hashed samples are sequenced again: + +```csv title="samplesheet.csv" +pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz +pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz +pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz +``` + ### Relative paths Using relative paths in a samplesheet is supported. From eb04c2b86020bd3c86a3b8c892b73a43f0ce5a92 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:46:18 +0200 Subject: [PATCH 55/90] Add more samples to example in README --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4d1c3208..e95a6b02 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,9 @@ For hashed PNA data (Proxiome kit v2), the samplesheet will look as follows: ```csv pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 -pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz +pool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz +pool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz ``` > [!NOTE] From dc26b27c975c80ae6f0c971a9e2c15e7af412dc0 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 09:58:29 +0200 Subject: [PATCH 56/90] Add missing warning about new naming scheme --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index e95a6b02..6fe9d573 100644 --- a/README.md +++ b/README.md @@ -45,9 +45,6 @@ The pipeline will run the following steps: > If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/), > which is the last version to support that data type. -> [!NOTE] -> TODO panel and design update 4.0 - > [!WARNING] > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. > This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable @@ -73,6 +70,12 @@ pool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001. > [!NOTE] > For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv) +> [!WARNING] +> Panel and design names have been completely renamed in pixelator 0.26 +> (nf-core/pixelator 4.0 and above). Refer to the pixelator +> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0) +> for more details. + Each row represents a sample and gives the design, a panel file and the input fastq files. Now, you can run the pipeline using: From 3fecc577459d7901beee3097662f2de5d97f06ad Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 10:01:30 +0200 Subject: [PATCH 57/90] Regenerate ro-crate after readme update --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index cbab4744..a3424df5 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-05-06T06:55:20+00:00", - "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. *(Conditional; only for PNA hashed data)* Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!NOTE]\n> TODO panel and design update 4.0\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz\n```\n\n>[!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", + "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz\n```\n\n> [!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\n> [!WARNING]\n> Panel and design names have been completely renamed in pixelator 0.26\n> (nf-core/pixelator 4.0 and above). Refer to the pixelator\n> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0)\n> for more details.\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { "@id": "main.nf" From ebe0f58bee1722804e3f3bb537af6f04456c7c6f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 11:04:03 +0200 Subject: [PATCH 58/90] Bump version to 4.0.0 --- .nf-core.yml | 2 +- CHANGELOG.md | 14 ++++++++++---- nextflow.config | 2 +- ro-crate-metadata.json | 18 +++++++++--------- 4 files changed, 21 insertions(+), 15 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index b6cb2636..c3ebd280 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -25,4 +25,4 @@ template: - fastqc - multiqc - igenomes - version: 3.1.0dev + version: 4.0.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 22352c2f..1c83d2a3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev - xxxx-xx-xx +## [[4.0.0](https://github.com/nf-core/pixelator/releases/tag/4.0.0)] - 2026-05-19 ### Added -- Proxiome V2 workflow by @Aratz [#204](https://github.com/nf-core/pixelator/pull/204), [#205](https://github.com/nf-core/pixelator/pull/205) +- Add Proxiome V2 workflow support, enabling sample pooling and processing of up to 8,000 cells per run by @Aratz [#204](https://github.com/nf-core/pixelator/pull/204), [#205](https://github.com/nf-core/pixelator/pull/205) ### Enhancements & fixes @@ -22,7 +22,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ------------- | ----------- | ----------- | | `pixelatorES` | 0.6.0 | 0.10.1 | -| `pixelatorES` | 0.23.0 | 0.26.0 | +| `pixelator` | 0.23.0 | 0.26.0 | + +> [!WARNING] +> Panel and design names have been completely renamed in pixelator 0.26 +> (nf-core/pixelator 4.0 and above). Refer to the pixelator +> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0) +> for more details. ### Parameters @@ -38,7 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 > Parameter has been **added** if just the new parameter information is present. > Parameter has been **removed** if new parameter information isn't present. -## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 +## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.1)] - 2026-03-09 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index ad816c6b..38e830ba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -370,7 +370,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '3.1.0dev' + version = '4.0.0' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index a3424df5..28a4414f 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-05-06T06:55:20+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2026-05-19T08:43:42+00:00", "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz\n```\n\n> [!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\n> [!WARNING]\n> Panel and design names have been completely renamed in pixelator 0.26\n> (nf-core/pixelator 4.0 and above). Refer to the pixelator\n> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0)\n> for more details.\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#1f0e5a5c-a69d-4fa1-bbfb-7944a5788635" + "@id": "#e1d538fd-160d-4bef-9279-564055014e49" } ], "name": "nf-core/pixelator" @@ -143,7 +143,7 @@ } ], "dateCreated": "", - "dateModified": "2026-05-06T08:55:20Z", + "dateModified": "2026-05-19T10:43:42Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -174,10 +174,10 @@ }, "url": [ "https://github.com/nf-core/pixelator", - "https://nf-co.re/pixelator/dev/" + "https://nf-co.re/pixelator/4.0.0/" ], "version": [ - "3.1.0dev" + "4.0.0" ] }, { @@ -193,11 +193,11 @@ "version": "!>=25.10.4" }, { - "@id": "#1f0e5a5c-a69d-4fa1-bbfb-7944a5788635", + "@id": "#e1d538fd-160d-4bef-9279-564055014e49", "@type": "TestSuite", "instance": [ { - "@id": "#9bd4a38f-6178-4402-bb21-8fc71be7f7bb" + "@id": "#f2105274-dcac-426b-96f7-fc9f2b3e504a" } ], "mainEntity": { @@ -206,7 +206,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#9bd4a38f-6178-4402-bb21-8fc71be7f7bb", + "@id": "#f2105274-dcac-426b-96f7-fc9f2b3e504a", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", From df63726687ee0721deefdf3c37e13d25e4161e61 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 11:51:08 +0200 Subject: [PATCH 59/90] Update snapshots --- tests/proxiome_v1.nf.test.snap | 8 ++++---- tests/proxiome_v2.nf.test.snap | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index a9f352f1..d02e5546 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -130,11 +130,11 @@ "pixelator": "0.26.0" }, "Workflow": { - "nf-core/pixelator": "v3.1.0dev" + "nf-core/pixelator": "v4.0.0" } } ], - "timestamp": "2026-05-13T14:43:44.938290509", + "timestamp": "2026-05-19T11:50:16.234033586", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -178,7 +178,7 @@ "pixelator": "0.26.0" }, "Workflow": { - "nf-core/pixelator": "v3.1.0dev" + "nf-core/pixelator": "v4.0.0" } }, [ @@ -273,7 +273,7 @@ "pixelator/sample_2.layout.pxl" ] ], - "timestamp": "2026-05-13T13:55:47.469820915", + "timestamp": "2026-05-19T11:48:56.493399385", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 1b38466d..f98dfec4 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -167,11 +167,11 @@ "pixelator": "0.26.0" }, "Workflow": { - "nf-core/pixelator": "v3.1.0dev" + "nf-core/pixelator": "v4.0.0" } } ], - "timestamp": "2026-05-18T11:00:46.039585674", + "timestamp": "2026-05-19T11:50:37.765871571", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -215,7 +215,7 @@ "pixelator": "0.26.0" }, "Workflow": { - "nf-core/pixelator": "v3.1.0dev" + "nf-core/pixelator": "v4.0.0" } }, [ @@ -357,7 +357,7 @@ "pixelator/sample_calling/sample4.report.json" ] ], - "timestamp": "2026-05-18T10:46:41.797306659", + "timestamp": "2026-05-19T11:49:07.544804495", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 64404955f55aacfcfa6297e164f860144f9fb036 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 14:24:54 +0200 Subject: [PATCH 60/90] Increase ci-runner volume back to 40GB The default volume was decreased from 30 to 40GB --- .github/workflows/nf-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c9b0e327..f9618471 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -64,6 +64,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 + - volume=40gb strategy: fail-fast: false matrix: From 34a0485004723fab1dc1b0ddfc6ef3ef339639cd Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 14:26:34 +0200 Subject: [PATCH 61/90] Temporarily allow singularity tests to run on dev --- .github/workflows/nf-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f9618471..0249e63d 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,11 +77,11 @@ jobs: exclude: - isMain: false profile: "conda" - - isMain: false - profile: "singularity" + #- isMain: false + # profile: "singularity" NXF_VER: - "25.10.4" - - "latest-everything" + #- "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} From 45d53dd0410473651e6e1809cf21c9ea0286bce4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 14:39:02 +0200 Subject: [PATCH 62/90] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 22352c2f..3f23f39a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) - Updated pixelatorES to 0.10.1 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197), [#204](https://github.com/nf-core/pixelator/pull/204) - Add `cells_1k` and `cells_8k` Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg [#202](https://github.com/nf-core/pixelator/pull/202) +- Fix singularity CI tests by @Aratz [#208](https://github.com/nf-core/pixelator/pull/208) ### Software dependencies From 825b10149c740f04a7d9c33734e072636a41625e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 14:44:49 +0200 Subject: [PATCH 63/90] Fix missing changelog entry --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f23f39a..688b20b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,8 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use `TMPDIR` when defined to store temporary files by @Aratz [#195](https://github.com/nf-core/pixelator/pull/195) - Retry experiment summary up to two times after failure by @Aratz [#196](https://github.com/nf-core/pixelator/pull/196) - Updated pixelatorES to 0.10.1 in PNA experiment summary step by @Aratz [#197](https://github.com/nf-core/pixelator/pull/197), [#204](https://github.com/nf-core/pixelator/pull/204) -- Add `cells_1k` and `cells_8k` Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg [#202](https://github.com/nf-core/pixelator/pull/202) +- Add `cells_1k` and `cells_8k` Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg [#203](https://github.com/nf-core/pixelator/pull/203) - Fix singularity CI tests by @Aratz [#208](https://github.com/nf-core/pixelator/pull/208) +- Update nf-core template to 4.0.2 by @Aratz [#202](https://github.com/nf-core/pixelator/pull/202) ### Software dependencies From ff820cd19374f50001fed58e3b02f182852eb3f0 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Tue, 19 May 2026 14:45:09 +0200 Subject: [PATCH 64/90] Revert "Temporarily allow singularity tests to run on dev" This reverts commit 34a0485004723fab1dc1b0ddfc6ef3ef339639cd. --- .github/workflows/nf-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 0249e63d..f9618471 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,11 +77,11 @@ jobs: exclude: - isMain: false profile: "conda" - #- isMain: false - # profile: "singularity" + - isMain: false + profile: "singularity" NXF_VER: - "25.10.4" - #- "latest-everything" + - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} From 7b9289cdb1fc84e0108c7f07f14e76bd1f43dcc3 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 08:00:19 +0200 Subject: [PATCH 65/90] Rename base_test.config -> test.config --- conf/{base_test.config => test.config} | 0 conf/test_proxiome_v1.config | 2 +- conf/test_proxiome_v2.config | 2 +- subworkflows/local/pna/v1/nextflow.config | 2 +- subworkflows/local/pna/v2/nextflow.config | 2 +- tests/nextflow.config | 2 +- 6 files changed, 5 insertions(+), 5 deletions(-) rename conf/{base_test.config => test.config} (100%) diff --git a/conf/base_test.config b/conf/test.config similarity index 100% rename from conf/base_test.config rename to conf/test.config diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index 9a9f6bb0..0e5bfb55 100644 --- a/conf/test_proxiome_v1.config +++ b/conf/test_proxiome_v1.config @@ -11,7 +11,7 @@ ---------------------------------------------------------------------------------------- */ -includeConfig 'base_test.config' +includeConfig 'test.config' params { config_profile_name = 'Test profile for proxiome v1 data' diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 2c38b6f3..9be1f07f 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -11,7 +11,7 @@ ---------------------------------------------------------------------------------------- */ -includeConfig 'base_test.config' +includeConfig 'test.config' params { config_profile_name = 'Test profile for proxiome v2 data' diff --git a/subworkflows/local/pna/v1/nextflow.config b/subworkflows/local/pna/v1/nextflow.config index 4122edb2..f40d109c 100644 --- a/subworkflows/local/pna/v1/nextflow.config +++ b/subworkflows/local/pna/v1/nextflow.config @@ -1,4 +1,4 @@ -includeConfig '../../../../conf/base_test.config' +includeConfig '../../../../conf/test.config' params.pna_demux_output_chunk_reads = "30K" params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/subworkflows/local/pna/v2/nextflow.config b/subworkflows/local/pna/v2/nextflow.config index 4122edb2..f40d109c 100644 --- a/subworkflows/local/pna/v2/nextflow.config +++ b/subworkflows/local/pna/v2/nextflow.config @@ -1,4 +1,4 @@ -includeConfig '../../../../conf/base_test.config' +includeConfig '../../../../conf/test.config' params.pna_demux_output_chunk_reads = "30K" params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/tests/nextflow.config b/tests/nextflow.config index e24c0e94..5c8d74df 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,7 +4,7 @@ ======================================================================================== */ -includeConfig '../conf/base_test.config' +includeConfig '../conf/test.config' aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 63f4b8b7aca0742662046af921577c25f7a931ee Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 08:57:21 +0200 Subject: [PATCH 66/90] Add documentation for container_env.config --- conf/container_env.config | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/conf/container_env.config b/conf/container_env.config index 9a1de411..f37a786b 100644 --- a/conf/container_env.config +++ b/conf/container_env.config @@ -1,3 +1,12 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Environment variables to be used inside containers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Specify location to use for temporary files. If available, `TMPDIR` will be + used, otherwise it will fallback on `/tmp`. +---------------------------------------------------------------------------------------- +*/ + env { MPLCONFIGDIR = '${TMPDIR:-/tmp}/.config/matplotlib' NUMBA_CACHE_DIR = '${TMPDIR:-/tmp}/.numba_cache' From ba2dd47a3e484c47ca8785b4fcede2c39aa6641b Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 09:16:34 +0200 Subject: [PATCH 67/90] Clarify nested test config imports --- conf/test_proxiome_v1.config | 1 + conf/test_proxiome_v2.config | 1 + subworkflows/local/pna/v1/nextflow.config | 1 + subworkflows/local/pna/v2/nextflow.config | 1 + tests/nextflow.config | 1 + 5 files changed, 5 insertions(+) diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index 0e5bfb55..fb998abf 100644 --- a/conf/test_proxiome_v1.config +++ b/conf/test_proxiome_v1.config @@ -11,6 +11,7 @@ ---------------------------------------------------------------------------------------- */ +// Include testdata base path, resource allocations and process configuration includeConfig 'test.config' params { diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 9be1f07f..56c5d589 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -11,6 +11,7 @@ ---------------------------------------------------------------------------------------- */ +// Include testdata base path, resource allocations and process configuration includeConfig 'test.config' params { diff --git a/subworkflows/local/pna/v1/nextflow.config b/subworkflows/local/pna/v1/nextflow.config index f40d109c..47a2cd6f 100644 --- a/subworkflows/local/pna/v1/nextflow.config +++ b/subworkflows/local/pna/v1/nextflow.config @@ -1,3 +1,4 @@ +// Include testdata base path, resource allocations and process configuration includeConfig '../../../../conf/test.config' params.pna_demux_output_chunk_reads = "30K" diff --git a/subworkflows/local/pna/v2/nextflow.config b/subworkflows/local/pna/v2/nextflow.config index f40d109c..47a2cd6f 100644 --- a/subworkflows/local/pna/v2/nextflow.config +++ b/subworkflows/local/pna/v2/nextflow.config @@ -1,3 +1,4 @@ +// Include testdata base path, resource allocations and process configuration includeConfig '../../../../conf/test.config' params.pna_demux_output_chunk_reads = "30K" diff --git a/tests/nextflow.config b/tests/nextflow.config index 5c8d74df..1171b445 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,6 +4,7 @@ ======================================================================================== */ +// Include testdata base path, resource allocations and process configuration includeConfig '../conf/test.config' aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 1012faabdb335f1485dea8e8d59185195900f9d9 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 09:41:35 +0200 Subject: [PATCH 68/90] Add pipeline specific contribution guidelines --- docs/CONTRIBUTING.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index e8aea4f3..f17f4c0a 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -176,3 +176,12 @@ nf-core pipelines bump-version --nextflow . #### Images and figures guidelines If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics). + +## Pipeline specific contribution guidelines + +nf-core/pixelator is built on top of mainly +[pixelator](https://github.com/PixelgenTechnologies/pixelator) and +[pixelatorES](https://github.com/PixelgenTechnologies/pixelatorES), two +products developed by Pixelgen Technologies. As open source projects, these +also welcome contributions from everyone. Please refer to the documentation of +these projects for more information. From bb9793a2ecccded40b17c7cacdde57d63582db30 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 09:42:33 +0200 Subject: [PATCH 69/90] Fix typo --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index e4a7d4da..4c7c6ff2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -15,7 +15,7 @@ Use this parameter to specify its location. --input '[path to samplesheet file]' ``` -We provide an example samplesheets for [Proxiome v1 data](../assets/samplesheet_proxiome_v1.csv) +We provide example samplesheets for [Proxiome v1 data](../assets/samplesheet_proxiome_v1.csv) and [Proxiome v2 data](../assets/samplesheet_proxiome_v2.csv), that can be used as a template to create your own samplesheet. From 939ed2308006056a19609379df5737797ffc9c28 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 13:30:43 +0200 Subject: [PATCH 70/90] Rename samplesheets in `assets/` --- ...esheet_proxiome_v1.csv => example_samplesheet_proxiome_v1.csv} | 0 ...esheet_proxiome_v2.csv => example_samplesheet_proxiome_v2.csv} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename assets/{samplesheet_proxiome_v1.csv => example_samplesheet_proxiome_v1.csv} (100%) rename assets/{samplesheet_proxiome_v2.csv => example_samplesheet_proxiome_v2.csv} (100%) diff --git a/assets/samplesheet_proxiome_v1.csv b/assets/example_samplesheet_proxiome_v1.csv similarity index 100% rename from assets/samplesheet_proxiome_v1.csv rename to assets/example_samplesheet_proxiome_v1.csv diff --git a/assets/samplesheet_proxiome_v2.csv b/assets/example_samplesheet_proxiome_v2.csv similarity index 100% rename from assets/samplesheet_proxiome_v2.csv rename to assets/example_samplesheet_proxiome_v2.csv From bbed8b727be408f0c9c7d13038c7420673c409e4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 14:49:46 +0200 Subject: [PATCH 71/90] Remove single-cell-pna subfolder --- conf/cells_1k.config | 10 ++-- conf/cells_8k.config | 10 ++-- conf/modules.pna.config | 16 +++--- .../{single-cell-pna => }/amplicon/main.nf | 2 +- .../{single-cell-pna => }/amplicon/meta.yml | 2 +- .../amplicon/tests/main.nf.test | 7 ++- .../amplicon/tests/main.nf.test.snap | 10 ++-- .../local/pixelator/amplicon/tests/tags.yml | 2 + .../{single-cell-pna => }/analysis/main.nf | 2 +- .../{single-cell-pna => }/analysis/meta.yml | 2 +- .../analysis/tests/main.nf.test | 7 ++- .../analysis/tests/main.nf.test.snap | 10 ++-- .../local/pixelator/analysis/tests/tags.yml | 2 + .../{single-cell-pna => }/collapse/main.nf | 2 +- .../{single-cell-pna => }/collapse/meta.yml | 2 +- .../collapse/tests/main.nf.test | 7 ++- .../collapse/tests/main.nf.test.snap | 10 ++-- .../local/pixelator/collapse/tests/tags.yml | 2 + .../combine_collapse/main.nf | 2 +- .../combine_collapse/meta.yml | 2 +- .../combine_collapse/tests/main.nf.test | 7 ++- .../combine_collapse/tests/main.nf.test.snap | 10 ++-- .../pixelator/combine_collapse/tests/tags.yml | 2 + .../{single-cell-pna => }/demux/main.nf | 2 +- .../{single-cell-pna => }/demux/meta.yml | 2 +- .../demux/tests/main.nf.test | 7 ++- .../demux/tests/main.nf.test.snap | 14 ++--- .../demux/tests/multiple_chunks.config | 2 +- modules/local/pixelator/demux/tests/tags.yml | 2 + .../{single-cell-pna => }/denoise/main.nf | 2 +- .../{single-cell-pna => }/denoise/meta.yml | 2 +- .../denoise/tests/main.nf.test | 7 ++- .../denoise/tests/main.nf.test.snap | 10 ++-- .../{single-cell-pna => }/graph/main.nf | 2 +- .../{single-cell-pna => }/graph/meta.yml | 2 +- .../graph/tests/main.nf.test | 7 ++- .../graph/tests/main.nf.test.snap | 10 ++-- modules/local/pixelator/graph/tests/tags.yml | 2 + .../{single-cell-pna => }/layout/main.nf | 2 +- .../{single-cell-pna => }/layout/meta.yml | 2 +- .../layout/tests/main.nf.test | 7 ++- .../layout/tests/main.nf.test.snap | 10 ++-- .../sample_calling/main.nf | 2 +- .../sample_calling/meta.yml | 2 +- .../sample_calling/tests/main.nf.test | 6 +-- .../sample_calling/tests/main.nf.test.snap | 6 +-- .../single-cell-pna/amplicon/tests/tags.yml | 2 - .../single-cell-pna/analysis/tests/tags.yml | 2 - .../single-cell-pna/collapse/tests/tags.yml | 2 - .../tests/multiple_chunks.config | 5 -- .../combine_collapse/tests/tags.yml | 2 - .../single-cell-pna/demux/tests/tags.yml | 2 - .../single-cell-pna/graph/tests/tags.yml | 2 - subworkflows/local/pna/v1/main.nf | 48 ++++++++--------- subworkflows/local/pna/v1/meta.yml | 16 +++--- .../local/pna/v1/tests/main.nf.test.snap | 2 +- subworkflows/local/pna/v2/main.nf | 54 +++++++++---------- subworkflows/local/pna/v2/meta.yml | 18 +++---- .../local/pna/v2/tests/main.nf.test.snap | 2 +- tests/scripts/run_tests_parallel.sh | 2 +- 60 files changed, 192 insertions(+), 205 deletions(-) rename modules/local/pixelator/{single-cell-pna => }/amplicon/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/amplicon/meta.yml (98%) rename modules/local/pixelator/{single-cell-pna => }/amplicon/tests/main.nf.test (93%) rename modules/local/pixelator/{single-cell-pna => }/amplicon/tests/main.nf.test.snap (95%) create mode 100644 modules/local/pixelator/amplicon/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/analysis/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/analysis/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/analysis/tests/main.nf.test (92%) rename modules/local/pixelator/{single-cell-pna => }/analysis/tests/main.nf.test.snap (96%) create mode 100644 modules/local/pixelator/analysis/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/collapse/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/collapse/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/collapse/tests/main.nf.test (96%) rename modules/local/pixelator/{single-cell-pna => }/collapse/tests/main.nf.test.snap (96%) create mode 100644 modules/local/pixelator/collapse/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/combine_collapse/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/combine_collapse/meta.yml (98%) rename modules/local/pixelator/{single-cell-pna => }/combine_collapse/tests/main.nf.test (94%) rename modules/local/pixelator/{single-cell-pna => }/combine_collapse/tests/main.nf.test.snap (94%) create mode 100644 modules/local/pixelator/combine_collapse/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/demux/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/demux/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/demux/tests/main.nf.test (96%) rename modules/local/pixelator/{single-cell-pna => }/demux/tests/main.nf.test.snap (96%) rename modules/local/pixelator/{single-cell-pna => }/demux/tests/multiple_chunks.config (62%) create mode 100644 modules/local/pixelator/demux/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/denoise/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/denoise/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/denoise/tests/main.nf.test (92%) rename modules/local/pixelator/{single-cell-pna => }/denoise/tests/main.nf.test.snap (96%) rename modules/local/pixelator/{single-cell-pna => }/graph/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/graph/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/graph/tests/main.nf.test (93%) rename modules/local/pixelator/{single-cell-pna => }/graph/tests/main.nf.test.snap (96%) create mode 100644 modules/local/pixelator/graph/tests/tags.yml rename modules/local/pixelator/{single-cell-pna => }/layout/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/layout/meta.yml (99%) rename modules/local/pixelator/{single-cell-pna => }/layout/tests/main.nf.test (93%) rename modules/local/pixelator/{single-cell-pna => }/layout/tests/main.nf.test.snap (96%) rename modules/local/pixelator/{single-cell-pna => }/sample_calling/main.nf (98%) rename modules/local/pixelator/{single-cell-pna => }/sample_calling/meta.yml (98%) rename modules/local/pixelator/{single-cell-pna => }/sample_calling/tests/main.nf.test (93%) rename modules/local/pixelator/{single-cell-pna => }/sample_calling/tests/main.nf.test.snap (97%) delete mode 100644 modules/local/pixelator/single-cell-pna/amplicon/tests/tags.yml delete mode 100644 modules/local/pixelator/single-cell-pna/analysis/tests/tags.yml delete mode 100644 modules/local/pixelator/single-cell-pna/collapse/tests/tags.yml delete mode 100644 modules/local/pixelator/single-cell-pna/combine_collapse/tests/multiple_chunks.config delete mode 100644 modules/local/pixelator/single-cell-pna/combine_collapse/tests/tags.yml delete mode 100644 modules/local/pixelator/single-cell-pna/demux/tests/tags.yml delete mode 100644 modules/local/pixelator/single-cell-pna/graph/tests/tags.yml diff --git a/conf/cells_1k.config b/conf/cells_1k.config index 5253119b..c958a93b 100644 --- a/conf/cells_1k.config +++ b/conf/cells_1k.config @@ -1,19 +1,19 @@ process { // All processes not defined here will rely on process labels and base.config. - withName: PIXELATOR_PNA_AMPLICON { + withName: PIXELATOR_AMPLICON { cpus = { 32 * task.attempt } memory = { 32.GB * task.attempt } time = { 4.h * task.attempt } } - withName: PIXELATOR_PNA_DEMUX { + withName: PIXELATOR_DEMUX { cpus = { 16 * task.attempt } memory = { 64.GB * task.attempt } time = { 4.h * task.attempt } } - withName: PIXELATOR_PNA_COLLAPSE { + withName: PIXELATOR_COLLAPSE { cpus = { 8 * task.attempt } memory = { 64.GB * task.attempt } time = { 8.h * task.attempt } @@ -21,7 +21,7 @@ process { errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } } - withName: PIXELATOR_PNA_COMBINE_COLLAPSE { + withName: PIXELATOR_COMBINE_COLLAPSE { cpus = { 16 * task.attempt } memory = { 128.GB * task.attempt } time = { 4.h * task.attempt } @@ -29,7 +29,7 @@ process { errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } } - withName: PIXELATOR_PNA_GRAPH { + withName: PIXELATOR_GRAPH { cpus = { 12 * task.attempt } memory = { 512.GB * task.attempt } time = { 10.h * task.attempt } diff --git a/conf/cells_8k.config b/conf/cells_8k.config index 4a592cf5..707e8bc2 100644 --- a/conf/cells_8k.config +++ b/conf/cells_8k.config @@ -1,19 +1,19 @@ process { // Keep process sizing overrides here for larger (8k cell) runs. - withName: PIXELATOR_PNA_AMPLICON { + withName: PIXELATOR_AMPLICON { cpus = { 32 * task.attempt } memory = { 32.GB * task.attempt } time = { 40.h * task.attempt } } - withName: PIXELATOR_PNA_DEMUX { + withName: PIXELATOR_DEMUX { cpus = { 16 * task.attempt } memory = { 128.GB * task.attempt } time = { 12.h * task.attempt } } - withName: PIXELATOR_PNA_COLLAPSE { + withName: PIXELATOR_COLLAPSE { cpus = { 8 * task.attempt } memory = { 256.GB * task.attempt } time = { 8.h * task.attempt } @@ -21,7 +21,7 @@ process { errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } } - withName: PIXELATOR_PNA_COMBINE_COLLAPSE { + withName: PIXELATOR_COMBINE_COLLAPSE { cpus = { 8 * task.attempt } memory = { 512.GB * task.attempt } time = { 6.h * task.attempt } @@ -29,7 +29,7 @@ process { errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 1) ? 'retry' : 'finish' } } - withName: PIXELATOR_PNA_GRAPH { + withName: PIXELATOR_GRAPH { cpus = { 12 * task.attempt } memory = { 512.GB * task.attempt } time = { 20.h * task.attempt } diff --git a/conf/modules.pna.config b/conf/modules.pna.config index dd52039d..e375298b 100644 --- a/conf/modules.pna.config +++ b/conf/modules.pna.config @@ -13,7 +13,7 @@ process { - withName: PIXELATOR_PNA_AMPLICON { + withName: PIXELATOR_AMPLICON { ext.args = { [ "--design ${meta.design}", @@ -48,7 +48,7 @@ process { ] } - withName: PIXELATOR_PNA_DEMUX { + withName: PIXELATOR_DEMUX { ext.args = { [ params.pna_demux_mismatches instanceof Integer ? "--mismatches ${params.pna_demux_mismatches}" : '', @@ -90,7 +90,7 @@ process { ] } - withName: PIXELATOR_PNA_COLLAPSE { + withName: PIXELATOR_COLLAPSE { ext.args = { [ params.pna_collapse_mismatches ? "--mismatches ${params.pna_collapse_mismatches}" : '', @@ -118,7 +118,7 @@ process { ] } - withName: PIXELATOR_PNA_GRAPH { + withName: PIXELATOR_GRAPH { ext.args = { [ params.pna_graph_multiplet_recovery ? "--multiplet-recovery" : '', @@ -155,7 +155,7 @@ process { ] } - withName: PIXELATOR_PNA_SAMPLE_CALLING { + withName: PIXELATOR_SAMPLE_CALLING { ext.args = { [ params.pna_sample_calling_remove_incompatible ? "--remove-incompatible" : '', @@ -184,7 +184,7 @@ process { ] } - withName: PIXELATOR_PNA_DENOISE { + withName: PIXELATOR_DENOISE { ext.when = { !params.skip_denoise } ext.args = { [ @@ -216,7 +216,7 @@ process { - withName: PIXELATOR_PNA_ANALYSIS { + withName: PIXELATOR_ANALYSIS { ext.when = { !params.skip_analysis } ext.args = { [ @@ -248,7 +248,7 @@ process { ] } - withName: PIXELATOR_PNA_LAYOUT { + withName: PIXELATOR_LAYOUT { ext.when = { !params.skip_layout } ext.args = { [ diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/amplicon/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/amplicon/main.nf rename to modules/local/pixelator/amplicon/main.nf index 7b40ad9e..fefe338b 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/main.nf +++ b/modules/local/pixelator/amplicon/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_AMPLICON { +process PIXELATOR_AMPLICON { tag "${meta.id}" label 'process_medium' diff --git a/modules/local/pixelator/single-cell-pna/amplicon/meta.yml b/modules/local/pixelator/amplicon/meta.yml similarity index 98% rename from modules/local/pixelator/single-cell-pna/amplicon/meta.yml rename to modules/local/pixelator/amplicon/meta.yml index ab24d3bc..d580765d 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/meta.yml +++ b/modules/local/pixelator/amplicon/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_amplicon +name: pixelator_amplicon description: Run `pixelator single-cell-pna amplicon` on input FASTQ files. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test b/modules/local/pixelator/amplicon/tests/main.nf.test similarity index 93% rename from modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test rename to modules/local/pixelator/amplicon/tests/main.nf.test index 84ea5a50..9f16a6cf 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test +++ b/modules/local/pixelator/amplicon/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_AMPLICON" + name "Test Process PIXELATOR_AMPLICON" script "../main.nf" - process "PIXELATOR_PNA_AMPLICON" + process "PIXELATOR_AMPLICON" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_amplicon" + tag "pixelator/amplicon" test("PNA amplicon - stub") { diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/amplicon/tests/main.nf.test.snap similarity index 95% rename from modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap rename to modules/local/pixelator/amplicon/tests/main.nf.test.snap index 8f546137..4f4dd938 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/amplicon/tests/main.nf.test.snap @@ -58,7 +58,7 @@ ], "5": [ [ - "PIXELATOR_PNA_AMPLICON", + "PIXELATOR_AMPLICON", "pixelator", "0.26.0" ] @@ -109,14 +109,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_AMPLICON", + "PIXELATOR_AMPLICON", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-12T16:46:59.439000448", + "timestamp": "2026-05-20T14:27:25.664498136", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -137,13 +137,13 @@ ], [ [ - "PIXELATOR_PNA_AMPLICON", + "PIXELATOR_AMPLICON", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:51:12.753868531", + "timestamp": "2026-05-20T14:27:49.821596738", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/amplicon/tests/tags.yml b/modules/local/pixelator/amplicon/tests/tags.yml new file mode 100644 index 00000000..951d203c --- /dev/null +++ b/modules/local/pixelator/amplicon/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/amplicon: + - modules/local/pixelator/amplicon/** diff --git a/modules/local/pixelator/single-cell-pna/analysis/main.nf b/modules/local/pixelator/analysis/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/analysis/main.nf rename to modules/local/pixelator/analysis/main.nf index b9c776e7..0a8f6e86 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/main.nf +++ b/modules/local/pixelator/analysis/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_ANALYSIS { +process PIXELATOR_ANALYSIS { tag "${meta.id}" label 'process_medium' diff --git a/modules/local/pixelator/single-cell-pna/analysis/meta.yml b/modules/local/pixelator/analysis/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/analysis/meta.yml rename to modules/local/pixelator/analysis/meta.yml index 7ea66469..16222f1d 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/meta.yml +++ b/modules/local/pixelator/analysis/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_analysis +name: pixelator_analysis description: Run `pixelator single-cell-pna analysis` on pixel data. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test b/modules/local/pixelator/analysis/tests/main.nf.test similarity index 92% rename from modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test rename to modules/local/pixelator/analysis/tests/main.nf.test index bcdad4cd..3f099139 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test +++ b/modules/local/pixelator/analysis/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_ANALYSIS" + name "Test Process PIXELATOR_ANALYSIS" script "../main.nf" - process "PIXELATOR_PNA_ANALYSIS" + process "PIXELATOR_ANALYSIS" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_analysis" + tag "pixelator/analysis" test("PNA analysis - stub") { diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap b/modules/local/pixelator/analysis/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap rename to modules/local/pixelator/analysis/tests/main.nf.test.snap index 1e1eb10b..2b0ea0ca 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/analysis/tests/main.nf.test.snap @@ -14,13 +14,13 @@ ], [ [ - "PIXELATOR_PNA_ANALYSIS", + "PIXELATOR_ANALYSIS", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:52:16.675506153", + "timestamp": "2026-05-20T14:28:25.911951216", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -100,7 +100,7 @@ ], "6": [ [ - "PIXELATOR_PNA_ANALYSIS", + "PIXELATOR_ANALYSIS", "pixelator", "0.26.0" ] @@ -166,14 +166,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_ANALYSIS", + "PIXELATOR_ANALYSIS", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:18:16.640765919", + "timestamp": "2026-05-20T14:27:59.265000672", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/analysis/tests/tags.yml b/modules/local/pixelator/analysis/tests/tags.yml new file mode 100644 index 00000000..7b55a59e --- /dev/null +++ b/modules/local/pixelator/analysis/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/analysis: + - modules/local/pixelator/analysis/** diff --git a/modules/local/pixelator/single-cell-pna/collapse/main.nf b/modules/local/pixelator/collapse/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/collapse/main.nf rename to modules/local/pixelator/collapse/main.nf index 510783ee..ae0b0f55 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/main.nf +++ b/modules/local/pixelator/collapse/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_COLLAPSE { +process PIXELATOR_COLLAPSE { tag "${meta.id}" label 'process_medium' diff --git a/modules/local/pixelator/single-cell-pna/collapse/meta.yml b/modules/local/pixelator/collapse/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/collapse/meta.yml rename to modules/local/pixelator/collapse/meta.yml index 808c7d54..c5ab74dd 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/meta.yml +++ b/modules/local/pixelator/collapse/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_collapse +name: pixelator_collapse description: Run `pixelator single-cell-pna collapse` to collapse reads into molecule-level parquet outputs. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test b/modules/local/pixelator/collapse/tests/main.nf.test similarity index 96% rename from modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test rename to modules/local/pixelator/collapse/tests/main.nf.test index 3f2d8183..331fa9bd 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test +++ b/modules/local/pixelator/collapse/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_COLLAPSE" + name "Test Process PIXELATOR_COLLAPSE" script "../main.nf" - process "PIXELATOR_PNA_COLLAPSE" + process "PIXELATOR_COLLAPSE" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_collapse" + tag "pixelator/collapse" test("PNA collapse - stub") { diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap b/modules/local/pixelator/collapse/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap rename to modules/local/pixelator/collapse/tests/main.nf.test.snap index dd9ef4fb..3027bca4 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/collapse/tests/main.nf.test.snap @@ -14,13 +14,13 @@ ], [ [ - "PIXELATOR_PNA_COLLAPSE", + "PIXELATOR_COLLAPSE", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:52:55.793377791", + "timestamp": "2026-05-20T14:28:49.824808507", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -89,7 +89,7 @@ ], "5": [ [ - "PIXELATOR_PNA_COLLAPSE", + "PIXELATOR_COLLAPSE", "pixelator", "0.26.0" ] @@ -144,14 +144,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_COLLAPSE", + "PIXELATOR_COLLAPSE", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:15:51.65572364", + "timestamp": "2026-05-20T14:28:34.287934812", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/collapse/tests/tags.yml b/modules/local/pixelator/collapse/tests/tags.yml new file mode 100644 index 00000000..44eaf569 --- /dev/null +++ b/modules/local/pixelator/collapse/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/collapse: + - modules/local/pixelator/collapse/** diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf b/modules/local/pixelator/combine_collapse/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/combine_collapse/main.nf rename to modules/local/pixelator/combine_collapse/main.nf index a683dabe..f427e040 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf +++ b/modules/local/pixelator/combine_collapse/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_COMBINE_COLLAPSE { +process PIXELATOR_COMBINE_COLLAPSE { tag "${meta.id}" label 'process_medium' diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml b/modules/local/pixelator/combine_collapse/meta.yml similarity index 98% rename from modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml rename to modules/local/pixelator/combine_collapse/meta.yml index 0da34349..1b64cf96 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/meta.yml +++ b/modules/local/pixelator/combine_collapse/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_combine_collapse +name: pixelator_combine_collapse description: Run `pixelator single-cell-pna combine-collapse` to merge multiple collapse outputs. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test b/modules/local/pixelator/combine_collapse/tests/main.nf.test similarity index 94% rename from modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test rename to modules/local/pixelator/combine_collapse/tests/main.nf.test index 9be59a29..15e2e383 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test @@ -1,13 +1,12 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_COMBINE_COLLAPSE" + name "Test Process PIXELATOR_COMBINE_COLLAPSE" script "../main.nf" - process "PIXELATOR_PNA_COMBINE_COLLAPSE" + process "PIXELATOR_COMBINE_COLLAPSE" tag "modules" tag "pixelator" - tag "pixelator/pna" tag "modules_pixelator" - tag "pixelator/single_cell_pna_combine_collapse" + tag "pixelator/combine_collapse" test("PNA combine collapse - stub") { diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap similarity index 94% rename from modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap rename to modules/local/pixelator/combine_collapse/tests/main.nf.test.snap index 46af2f92..1b3dd56a 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap @@ -13,13 +13,13 @@ ], [ [ - "PIXELATOR_PNA_COMBINE_COLLAPSE", + "PIXELATOR_COMBINE_COLLAPSE", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T08:16:53.369689781", + "timestamp": "2026-05-20T14:29:29.978160031", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -84,7 +84,7 @@ ], "5": [ [ - "PIXELATOR_PNA_COMBINE_COLLAPSE", + "PIXELATOR_COMBINE_COLLAPSE", "pixelator", "0.26.0" ] @@ -135,14 +135,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_COMBINE_COLLAPSE", + "PIXELATOR_COMBINE_COLLAPSE", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:16:36.538161388", + "timestamp": "2026-05-20T14:29:17.917223368", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/combine_collapse/tests/tags.yml b/modules/local/pixelator/combine_collapse/tests/tags.yml new file mode 100644 index 00000000..dfb7bcad --- /dev/null +++ b/modules/local/pixelator/combine_collapse/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/combine_collapse: + - modules/local/pixelator/combine_collapse/** diff --git a/modules/local/pixelator/single-cell-pna/demux/main.nf b/modules/local/pixelator/demux/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/demux/main.nf rename to modules/local/pixelator/demux/main.nf index 5703b013..dd5ce74e 100644 --- a/modules/local/pixelator/single-cell-pna/demux/main.nf +++ b/modules/local/pixelator/demux/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_DEMUX { +process PIXELATOR_DEMUX { tag "${meta.id}" label 'process_medium' diff --git a/modules/local/pixelator/single-cell-pna/demux/meta.yml b/modules/local/pixelator/demux/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/demux/meta.yml rename to modules/local/pixelator/demux/meta.yml index 07de6b84..a138345f 100644 --- a/modules/local/pixelator/single-cell-pna/demux/meta.yml +++ b/modules/local/pixelator/demux/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_demux +name: pixelator_demux description: Run `pixelator single-cell-pna demux` to split reads and generate demultiplexed outputs. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test b/modules/local/pixelator/demux/tests/main.nf.test similarity index 96% rename from modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test rename to modules/local/pixelator/demux/tests/main.nf.test index d5e3c6ac..dacc77e8 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test +++ b/modules/local/pixelator/demux/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_DEMUX" + name "Test Process PIXELATOR_DEMUX" script "../main.nf" - process "PIXELATOR_PNA_DEMUX" + process "PIXELATOR_DEMUX" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_demux" + tag "pixelator/demux" test("PNA demux - stub") { diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap b/modules/local/pixelator/demux/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap rename to modules/local/pixelator/demux/tests/main.nf.test.snap index 106f4bae..e08d02ad 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/demux/tests/main.nf.test.snap @@ -17,13 +17,13 @@ ], [ [ - "PIXELATOR_PNA_DEMUX", + "PIXELATOR_DEMUX", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:54:49.604614166", + "timestamp": "2026-05-20T14:30:04.325516148", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -116,7 +116,7 @@ ], "7": [ [ - "PIXELATOR_PNA_DEMUX", + "PIXELATOR_DEMUX", "pixelator", "0.26.0" ] @@ -192,14 +192,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_DEMUX", + "PIXELATOR_DEMUX", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:14:52.528292928", + "timestamp": "2026-05-20T14:29:38.959759778", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -237,13 +237,13 @@ ], [ [ - "PIXELATOR_PNA_DEMUX", + "PIXELATOR_DEMUX", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:55:28.928009264", + "timestamp": "2026-05-20T14:30:29.692789975", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/multiple_chunks.config b/modules/local/pixelator/demux/tests/multiple_chunks.config similarity index 62% rename from modules/local/pixelator/single-cell-pna/demux/tests/multiple_chunks.config rename to modules/local/pixelator/demux/tests/multiple_chunks.config index 4cffec50..6a12f124 100644 --- a/modules/local/pixelator/single-cell-pna/demux/tests/multiple_chunks.config +++ b/modules/local/pixelator/demux/tests/multiple_chunks.config @@ -1,5 +1,5 @@ process { - withName: "PIXELATOR_PNA_DEMUX" { + withName: "PIXELATOR_DEMUX" { ext.args = "--output-chunk-reads 40K" } } diff --git a/modules/local/pixelator/demux/tests/tags.yml b/modules/local/pixelator/demux/tests/tags.yml new file mode 100644 index 00000000..437d9ed8 --- /dev/null +++ b/modules/local/pixelator/demux/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/demux: + - modules/local/pixelator/demux/** diff --git a/modules/local/pixelator/single-cell-pna/denoise/main.nf b/modules/local/pixelator/denoise/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/denoise/main.nf rename to modules/local/pixelator/denoise/main.nf index fecb1385..3018a54d 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/main.nf +++ b/modules/local/pixelator/denoise/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_DENOISE { +process PIXELATOR_DENOISE { tag "$meta.id" label 'process_high' diff --git a/modules/local/pixelator/single-cell-pna/denoise/meta.yml b/modules/local/pixelator/denoise/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/denoise/meta.yml rename to modules/local/pixelator/denoise/meta.yml index 783497f4..714730c8 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/meta.yml +++ b/modules/local/pixelator/denoise/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_denoise +name: pixelator_denoise description: Run `pixelator single-cell-pna denoise` on graph output data. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test b/modules/local/pixelator/denoise/tests/main.nf.test similarity index 92% rename from modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test rename to modules/local/pixelator/denoise/tests/main.nf.test index fd5eb381..b6c383cf 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test +++ b/modules/local/pixelator/denoise/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_DENOISE" + name "Test Process PIXELATOR_DENOISE" script "../main.nf" - process "PIXELATOR_PNA_DENOISE" + process "PIXELATOR_DENOISE" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_denoise" + tag "pixelator/denoise" test("PNA denoise - stub") { diff --git a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap b/modules/local/pixelator/denoise/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap rename to modules/local/pixelator/denoise/tests/main.nf.test.snap index a3e5d7bf..447a75f9 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/denoise/tests/main.nf.test.snap @@ -13,13 +13,13 @@ ], [ [ - "PIXELATOR_PNA_DENOISE", + "PIXELATOR_DENOISE", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T08:18:06.55044623", + "timestamp": "2026-05-20T14:30:51.886838398", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -99,7 +99,7 @@ ], "6": [ [ - "PIXELATOR_PNA_DENOISE", + "PIXELATOR_DENOISE", "pixelator", "0.26.0" ] @@ -165,14 +165,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_DENOISE", + "PIXELATOR_DENOISE", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:17:51.870638966", + "timestamp": "2026-05-20T14:30:37.793498942", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/single-cell-pna/graph/main.nf b/modules/local/pixelator/graph/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/graph/main.nf rename to modules/local/pixelator/graph/main.nf index c02b63bf..0ccc74f8 100644 --- a/modules/local/pixelator/single-cell-pna/graph/main.nf +++ b/modules/local/pixelator/graph/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_GRAPH { +process PIXELATOR_GRAPH { tag "${meta.id}" label 'process_high_memory' label 'process_long' diff --git a/modules/local/pixelator/single-cell-pna/graph/meta.yml b/modules/local/pixelator/graph/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/graph/meta.yml rename to modules/local/pixelator/graph/meta.yml index 5b78eae0..a2846c98 100644 --- a/modules/local/pixelator/single-cell-pna/graph/meta.yml +++ b/modules/local/pixelator/graph/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_graph +name: pixelator_graph description: Run `pixelator single-cell-pna graph` to build graph-level pixel files. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test b/modules/local/pixelator/graph/tests/main.nf.test similarity index 93% rename from modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test rename to modules/local/pixelator/graph/tests/main.nf.test index ab8f7e5f..2a68005a 100644 --- a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test +++ b/modules/local/pixelator/graph/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_GRAPH" + name "Test Process PIXELATOR_GRAPH" script "../main.nf" - process "PIXELATOR_PNA_GRAPH" + process "PIXELATOR_GRAPH" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_graph" + tag "pixelator/graph" test("PNA graph - stub") { diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap b/modules/local/pixelator/graph/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap rename to modules/local/pixelator/graph/tests/main.nf.test.snap index bf1fee4f..612d911f 100644 --- a/modules/local/pixelator/single-cell-pna/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/graph/tests/main.nf.test.snap @@ -73,7 +73,7 @@ ], "6": [ [ - "PIXELATOR_PNA_GRAPH", + "PIXELATOR_GRAPH", "pixelator", "0.26.0" ] @@ -139,14 +139,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_GRAPH", + "PIXELATOR_GRAPH", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:17:03.182656139", + "timestamp": "2026-05-20T14:31:00.131846199", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -167,13 +167,13 @@ ], [ [ - "PIXELATOR_PNA_GRAPH", + "PIXELATOR_GRAPH", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T13:56:21.604809809", + "timestamp": "2026-05-20T14:31:17.955182089", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/graph/tests/tags.yml b/modules/local/pixelator/graph/tests/tags.yml new file mode 100644 index 00000000..5688ce02 --- /dev/null +++ b/modules/local/pixelator/graph/tests/tags.yml @@ -0,0 +1,2 @@ +pixelator/graph: + - modules/local/pixelator/graph/** diff --git a/modules/local/pixelator/single-cell-pna/layout/main.nf b/modules/local/pixelator/layout/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/layout/main.nf rename to modules/local/pixelator/layout/main.nf index 7e98cf34..fecb0f68 100644 --- a/modules/local/pixelator/single-cell-pna/layout/main.nf +++ b/modules/local/pixelator/layout/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_LAYOUT { +process PIXELATOR_LAYOUT { tag "${meta.id}" label 'process_high' diff --git a/modules/local/pixelator/single-cell-pna/layout/meta.yml b/modules/local/pixelator/layout/meta.yml similarity index 99% rename from modules/local/pixelator/single-cell-pna/layout/meta.yml rename to modules/local/pixelator/layout/meta.yml index 93cec7b9..75eb3a9e 100644 --- a/modules/local/pixelator/single-cell-pna/layout/meta.yml +++ b/modules/local/pixelator/layout/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_layout +name: pixelator_layout description: Run `pixelator single-cell-pna layout` to compute layout outputs from pixel data. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test b/modules/local/pixelator/layout/tests/main.nf.test similarity index 93% rename from modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test rename to modules/local/pixelator/layout/tests/main.nf.test index 429d45ea..db2f832a 100644 --- a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test +++ b/modules/local/pixelator/layout/tests/main.nf.test @@ -1,12 +1,11 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_LAYOUT" + name "Test Process PIXELATOR_LAYOUT" script "../main.nf" - process "PIXELATOR_PNA_LAYOUT" + process "PIXELATOR_LAYOUT" tag "modules" tag "pixelator" - tag "pixelator/pna" - tag "pixelator/single_cell_pna_layout" + tag "pixelator/layout" test("Test PNA layout - stub") { diff --git a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap b/modules/local/pixelator/layout/tests/main.nf.test.snap similarity index 96% rename from modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap rename to modules/local/pixelator/layout/tests/main.nf.test.snap index 78ed74dc..41951b62 100644 --- a/modules/local/pixelator/single-cell-pna/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/layout/tests/main.nf.test.snap @@ -14,13 +14,13 @@ ], [ [ - "PIXELATOR_PNA_LAYOUT", + "PIXELATOR_LAYOUT", "pixelator", "0.26.0" ] ] ], - "timestamp": "2026-05-13T08:19:06.474778967", + "timestamp": "2026-05-20T14:31:41.190244206", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -100,7 +100,7 @@ ], "6": [ [ - "PIXELATOR_PNA_LAYOUT", + "PIXELATOR_LAYOUT", "pixelator", "0.26.0" ] @@ -166,14 +166,14 @@ ], "versions_pixelator": [ [ - "PIXELATOR_PNA_LAYOUT", + "PIXELATOR_LAYOUT", "pixelator", "0.26.0" ] ] } ], - "timestamp": "2026-05-13T08:18:51.955991713", + "timestamp": "2026-05-20T14:31:26.577414445", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf b/modules/local/pixelator/sample_calling/main.nf similarity index 98% rename from modules/local/pixelator/single-cell-pna/sample_calling/main.nf rename to modules/local/pixelator/sample_calling/main.nf index 06f26cdb..efc7b9ff 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/main.nf +++ b/modules/local/pixelator/sample_calling/main.nf @@ -1,4 +1,4 @@ -process PIXELATOR_PNA_SAMPLE_CALLING { +process PIXELATOR_SAMPLE_CALLING { tag "${meta.id}" label 'process_high' diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/meta.yml b/modules/local/pixelator/sample_calling/meta.yml similarity index 98% rename from modules/local/pixelator/single-cell-pna/sample_calling/meta.yml rename to modules/local/pixelator/sample_calling/meta.yml index 1291c50a..cf904a9b 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/meta.yml +++ b/modules/local/pixelator/sample_calling/meta.yml @@ -1,4 +1,4 @@ -name: pixelator_pna_sample_calling +name: pixelator_sample_calling description: Run `pixelator single-cell-pna sample-calling` to split data into sample-level pixel files. keywords: - pixelator diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test b/modules/local/pixelator/sample_calling/tests/main.nf.test similarity index 93% rename from modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test rename to modules/local/pixelator/sample_calling/tests/main.nf.test index 9dba1c11..aff4ddf5 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test @@ -1,12 +1,12 @@ nextflow_process { - name "Test Process PIXELATOR_PNA_SAMPLE_CALLING" + name "Test Process PIXELATOR_SAMPLE_CALLING" script "../main.nf" - process "PIXELATOR_PNA_SAMPLE_CALLING" + process "PIXELATOR_SAMPLE_CALLING" tag "modules" tag "pixelator" tag "pixelator/pna" - tag "pixelator/single_cell_pna_sample_calling" + tag "pixelator/sample_calling" test("PNA sample calling - stub") { diff --git a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap similarity index 97% rename from modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap rename to modules/local/pixelator/sample_calling/tests/main.nf.test.snap index fbf2cef3..0a7659b9 100644 --- a/modules/local/pixelator/single-cell-pna/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap @@ -110,7 +110,7 @@ ] ], "6": [ - "versions.yml:md5,ae6f55a43baabae8e12ad36f7860bdfe" + "versions.yml:md5,7c42eee900660ec5bcdc04fbbb2e2e3e" ], "all_results": [ [ @@ -180,11 +180,11 @@ ] ], "versions": [ - "versions.yml:md5,ae6f55a43baabae8e12ad36f7860bdfe" + "versions.yml:md5,7c42eee900660ec5bcdc04fbbb2e2e3e" ] } ], - "timestamp": "2026-05-18T16:07:27.561906124", + "timestamp": "2026-05-20T14:31:49.737316113", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/single-cell-pna/amplicon/tests/tags.yml b/modules/local/pixelator/single-cell-pna/amplicon/tests/tags.yml deleted file mode 100644 index dc533a28..00000000 --- a/modules/local/pixelator/single-cell-pna/amplicon/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_amplicon: - - modules/local/pixelator/single-cell-pna/amplicon/** diff --git a/modules/local/pixelator/single-cell-pna/analysis/tests/tags.yml b/modules/local/pixelator/single-cell-pna/analysis/tests/tags.yml deleted file mode 100644 index 12f2ae52..00000000 --- a/modules/local/pixelator/single-cell-pna/analysis/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_analysis: - - modules/local/pixelator/single-cell-pna/analysis/** diff --git a/modules/local/pixelator/single-cell-pna/collapse/tests/tags.yml b/modules/local/pixelator/single-cell-pna/collapse/tests/tags.yml deleted file mode 100644 index b5e97eb0..00000000 --- a/modules/local/pixelator/single-cell-pna/collapse/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_collapse: - - modules/local/pixelator/single-cell-pna/collapse/** diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/multiple_chunks.config b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/multiple_chunks.config deleted file mode 100644 index 89181d1c..00000000 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/multiple_chunks.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: "PIXELATOR_PNA_DEMUX" { - ext.args = "--output-chunk-size 40K" - } -} diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/tags.yml b/modules/local/pixelator/single-cell-pna/combine_collapse/tests/tags.yml deleted file mode 100644 index c2b7a926..00000000 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_demux: - - modules/local/pixelator/single-cell-pna/demux/** diff --git a/modules/local/pixelator/single-cell-pna/demux/tests/tags.yml b/modules/local/pixelator/single-cell-pna/demux/tests/tags.yml deleted file mode 100644 index c2b7a926..00000000 --- a/modules/local/pixelator/single-cell-pna/demux/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_demux: - - modules/local/pixelator/single-cell-pna/demux/** diff --git a/modules/local/pixelator/single-cell-pna/graph/tests/tags.yml b/modules/local/pixelator/single-cell-pna/graph/tests/tags.yml deleted file mode 100644 index a3b68c3c..00000000 --- a/modules/local/pixelator/single-cell-pna/graph/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/single_cell_pna_graph: - - modules/local/pixelator/single-cell-pna/graph/** diff --git a/subworkflows/local/pna/v1/main.nf b/subworkflows/local/pna/v1/main.nf index e7cfde53..81eccb60 100644 --- a/subworkflows/local/pna/v1/main.nf +++ b/subworkflows/local/pna/v1/main.nf @@ -16,14 +16,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PIXELATOR_PNA_AMPLICON } from '../../../../modules/local/pixelator/single-cell-pna/amplicon/main' -include { PIXELATOR_PNA_DEMUX } from '../../../../modules/local/pixelator/single-cell-pna/demux/main' -include { PIXELATOR_PNA_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/collapse/main' -include { PIXELATOR_PNA_GRAPH } from '../../../../modules/local/pixelator/single-cell-pna/graph/main' -include { PIXELATOR_PNA_DENOISE } from '../../../../modules/local/pixelator/single-cell-pna/denoise/main' -include { PIXELATOR_PNA_ANALYSIS } from '../../../../modules/local/pixelator/single-cell-pna/analysis/main' -include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/combine_collapse/main' -include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout/main' +include { PIXELATOR_AMPLICON } from '../../../../modules/local/pixelator/amplicon/main' +include { PIXELATOR_DEMUX } from '../../../../modules/local/pixelator/demux/main' +include { PIXELATOR_COLLAPSE } from '../../../../modules/local/pixelator/collapse/main' +include { PIXELATOR_GRAPH } from '../../../../modules/local/pixelator/graph/main' +include { PIXELATOR_DENOISE } from '../../../../modules/local/pixelator/denoise/main' +include { PIXELATOR_ANALYSIS } from '../../../../modules/local/pixelator/analysis/main' +include { PIXELATOR_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/combine_collapse/main' +include { PIXELATOR_LAYOUT } from '../../../../modules/local/pixelator/layout/main' include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main' /* @@ -98,8 +98,8 @@ workflow PIXELATOR_PNA_V1 { // // MODULE: Run pixelator single-cell-pna amplicon // - PIXELATOR_PNA_AMPLICON ( ch_cat_fastq ) - ch_amplicon = PIXELATOR_PNA_AMPLICON.out.amplicon + PIXELATOR_AMPLICON ( ch_cat_fastq ) + ch_amplicon = PIXELATOR_AMPLICON.out.amplicon // // MODULE: Run pixelator single-cell demux @@ -109,8 +109,8 @@ workflow PIXELATOR_PNA_V1 { .map { meta, fq, panel_file -> [meta, fq, panel_file, meta.panel, meta.design] } - PIXELATOR_PNA_DEMUX(ch_demux_input) - ch_demuxed = PIXELATOR_PNA_DEMUX.out.demuxed + PIXELATOR_DEMUX(ch_demux_input) + ch_demuxed = PIXELATOR_DEMUX.out.demuxed // // MODULE: Run pixelator single-cell collapse @@ -129,9 +129,9 @@ workflow PIXELATOR_PNA_V1 { .flatMap() - PIXELATOR_PNA_COLLAPSE(ch_collapse_input) - ch_collapsed = PIXELATOR_PNA_COLLAPSE.out.collapsed - ch_collapsed_reports = PIXELATOR_PNA_COLLAPSE.out.report_json + PIXELATOR_COLLAPSE(ch_collapse_input) + ch_collapsed = PIXELATOR_COLLAPSE.out.collapsed + ch_collapsed_reports = PIXELATOR_COLLAPSE.out.report_json // Collect the partitioned collapse.parquet files in a list per sample // use the dynamic size information from `meta.parts` to group the files @@ -157,11 +157,11 @@ workflow PIXELATOR_PNA_V1 { } - PIXELATOR_PNA_COMBINE_COLLAPSE(ch_collapse_combine_split.multi) + PIXELATOR_COMBINE_COLLAPSE(ch_collapse_combine_split.multi) ch_combined_collapsed = ch_collapse_combine_split.single .map { meta, parquet, _reports -> [meta, parquet] } - .mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.parquet) + .mix(PIXELATOR_COMBINE_COLLAPSE.out.parquet) // // MODULE: Run pixelator single-cell graph @@ -170,27 +170,27 @@ workflow PIXELATOR_PNA_V1 { .join(ch_panel_files) .map { meta, parquet, panel_file -> [meta, parquet, panel_file, panel_file ? null : meta.panel] } - PIXELATOR_PNA_GRAPH(ch_graph_input) - ch_graph = PIXELATOR_PNA_GRAPH.out.pixelfile + PIXELATOR_GRAPH(ch_graph_input) + ch_graph = PIXELATOR_GRAPH.out.pixelfile // // MODULE: Run pixelator single-cell denoise // - PIXELATOR_PNA_DENOISE ( ch_graph ) - ch_denoise = PIXELATOR_PNA_DENOISE.out.pixelfile + PIXELATOR_DENOISE ( ch_graph ) + ch_denoise = PIXELATOR_DENOISE.out.pixelfile // // MODULE: Run pixelator single-cell analysis // ch_analysis_input = params.skip_denoise ? ch_graph : ch_denoise - PIXELATOR_PNA_ANALYSIS(ch_analysis_input) - ch_analysis = PIXELATOR_PNA_ANALYSIS.out.pixelfile + PIXELATOR_ANALYSIS(ch_analysis_input) + ch_analysis = PIXELATOR_ANALYSIS.out.pixelfile // // MODULE: Run pixelator single-cell layout // - PIXELATOR_PNA_LAYOUT(ch_analysis) + PIXELATOR_LAYOUT(ch_analysis) // Prepare all data needed by reporting for each pixelator step ch_input = channel.fromPath(params.input) diff --git a/subworkflows/local/pna/v1/meta.yml b/subworkflows/local/pna/v1/meta.yml index ed407abf..b0cbc6e1 100644 --- a/subworkflows/local/pna/v1/meta.yml +++ b/subworkflows/local/pna/v1/meta.yml @@ -8,14 +8,14 @@ keywords: - fastq components: - cat/fastq - - pixelator/pna/amplicon - - pixelator/pna/demux - - pixelator/pna/collapse - - pixelator/pna/combine/collapse - - pixelator/pna/graph - - pixelator/pna/denoise - - pixelator/pna/analysis - - pixelator/pna/layout + - pixelator/amplicon + - pixelator/demux + - pixelator/collapse + - pixelator/combine/collapse + - pixelator/graph + - pixelator/denoise + - pixelator/analysis + - pixelator/layout - experiment/summary - pna_generate_reports input: diff --git a/subworkflows/local/pna/v1/tests/main.nf.test.snap b/subworkflows/local/pna/v1/tests/main.nf.test.snap index 596d83a7..a566050a 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v1/tests/main.nf.test.snap @@ -92,7 +92,7 @@ "pixelator/logs/sample1.pixelator-layout.log" ] ], - "timestamp": "2026-05-13T09:31:53.768855272", + "timestamp": "2026-05-20T14:22:55.637136331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/local/pna/v2/main.nf b/subworkflows/local/pna/v2/main.nf index 8b56e83a..4a38203e 100644 --- a/subworkflows/local/pna/v2/main.nf +++ b/subworkflows/local/pna/v2/main.nf @@ -16,15 +16,15 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PIXELATOR_PNA_AMPLICON } from '../../../../modules/local/pixelator/single-cell-pna/amplicon' -include { PIXELATOR_PNA_DEMUX } from '../../../../modules/local/pixelator/single-cell-pna/demux' -include { PIXELATOR_PNA_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/collapse' -include { PIXELATOR_PNA_GRAPH } from '../../../../modules/local/pixelator/single-cell-pna/graph' -include { PIXELATOR_PNA_SAMPLE_CALLING } from '../../../../modules/local/pixelator/single-cell-pna/sample_calling' -include { PIXELATOR_PNA_DENOISE } from '../../../../modules/local/pixelator/single-cell-pna/denoise' -include { PIXELATOR_PNA_ANALYSIS } from '../../../../modules/local/pixelator/single-cell-pna/analysis' -include { PIXELATOR_PNA_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/single-cell-pna/combine_collapse' -include { PIXELATOR_PNA_LAYOUT } from '../../../../modules/local/pixelator/single-cell-pna/layout' +include { PIXELATOR_AMPLICON } from '../../../../modules/local/pixelator/amplicon' +include { PIXELATOR_DEMUX } from '../../../../modules/local/pixelator/demux' +include { PIXELATOR_COLLAPSE } from '../../../../modules/local/pixelator/collapse' +include { PIXELATOR_GRAPH } from '../../../../modules/local/pixelator/graph' +include { PIXELATOR_SAMPLE_CALLING } from '../../../../modules/local/pixelator/sample_calling' +include { PIXELATOR_DENOISE } from '../../../../modules/local/pixelator/denoise' +include { PIXELATOR_ANALYSIS } from '../../../../modules/local/pixelator/analysis' +include { PIXELATOR_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/combine_collapse' +include { PIXELATOR_LAYOUT } from '../../../../modules/local/pixelator/layout' include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main' @@ -122,8 +122,8 @@ workflow PIXELATOR_PNA_V2 { // // MODULE: Run pixelator single-cell-pna amplicon // - PIXELATOR_PNA_AMPLICON ( ch_cat_fastq ) - ch_amplicon = PIXELATOR_PNA_AMPLICON.out.amplicon + PIXELATOR_AMPLICON ( ch_cat_fastq ) + ch_amplicon = PIXELATOR_AMPLICON.out.amplicon // // MODULE: Run pixelator single-cell demux @@ -133,8 +133,8 @@ workflow PIXELATOR_PNA_V2 { .map { meta, fq, panel_file -> [meta, fq, panel_file, meta.panel, meta.design] } - PIXELATOR_PNA_DEMUX(ch_demux_input) - ch_demuxed = PIXELATOR_PNA_DEMUX.out.demuxed + PIXELATOR_DEMUX(ch_demux_input) + ch_demuxed = PIXELATOR_DEMUX.out.demuxed // // MODULE: Run pixelator single-cell collapse @@ -153,9 +153,9 @@ workflow PIXELATOR_PNA_V2 { .flatMap() - PIXELATOR_PNA_COLLAPSE(ch_collapse_input) - ch_collapsed = PIXELATOR_PNA_COLLAPSE.out.collapsed - ch_collapsed_reports = PIXELATOR_PNA_COLLAPSE.out.report_json + PIXELATOR_COLLAPSE(ch_collapse_input) + ch_collapsed = PIXELATOR_COLLAPSE.out.collapsed + ch_collapsed_reports = PIXELATOR_COLLAPSE.out.report_json // Collect the partitioned collapse.parquet files in a list per sample // use the dynamic size information from `meta.parts` to group the files @@ -180,11 +180,11 @@ workflow PIXELATOR_PNA_V2 { } - PIXELATOR_PNA_COMBINE_COLLAPSE(ch_collapse_combine_split.multi) + PIXELATOR_COMBINE_COLLAPSE(ch_collapse_combine_split.multi) ch_combined_collapsed = ch_collapse_combine_split.single .map { meta, parquet, _reports -> [meta, parquet] } - .mix(PIXELATOR_PNA_COMBINE_COLLAPSE.out.parquet) + .mix(PIXELATOR_COMBINE_COLLAPSE.out.parquet) // // MODULE: Run pixelator single-cell graph @@ -193,8 +193,8 @@ workflow PIXELATOR_PNA_V2 { .join(ch_panel_files_grouped_by_pool) .map { meta, parquet, panel_file -> [meta, parquet, panel_file, panel_file ? null : meta.panel] } - PIXELATOR_PNA_GRAPH(ch_graph_input) - ch_graph = PIXELATOR_PNA_GRAPH.out.pixelfile + PIXELATOR_GRAPH(ch_graph_input) + ch_graph = PIXELATOR_GRAPH.out.pixelfile // // MODULE: Run pixelator single-cell sample-calling @@ -202,8 +202,8 @@ workflow PIXELATOR_PNA_V2 { ch_sample_calling_input = ch_graph .map { meta, parquet -> [meta, parquet, file(params.input)] } - PIXELATOR_PNA_SAMPLE_CALLING (ch_sample_calling_input) - ch_sample_called = PIXELATOR_PNA_SAMPLE_CALLING.out.pixelfile + PIXELATOR_SAMPLE_CALLING (ch_sample_calling_input) + ch_sample_called = PIXELATOR_SAMPLE_CALLING.out.pixelfile // Extract the sample names from the pixel file names so that we can // merge them in with the panel file names correctly @@ -223,21 +223,21 @@ workflow PIXELATOR_PNA_V2 { // // MODULE: Run pixelator single-cell denoise // - PIXELATOR_PNA_DENOISE ( ch_sample_called ) - ch_denoise = PIXELATOR_PNA_DENOISE.out.pixelfile + PIXELATOR_DENOISE ( ch_sample_called ) + ch_denoise = PIXELATOR_DENOISE.out.pixelfile // // MODULE: Run pixelator single-cell analysis // ch_analysis_input = params.skip_denoise ? ch_sample_called : ch_denoise - PIXELATOR_PNA_ANALYSIS ( ch_analysis_input ) - ch_analysis = PIXELATOR_PNA_ANALYSIS.out.pixelfile + PIXELATOR_ANALYSIS ( ch_analysis_input ) + ch_analysis = PIXELATOR_ANALYSIS.out.pixelfile // // MODULE: Run pixelator single-cell layout // - PIXELATOR_PNA_LAYOUT( ch_analysis ) + PIXELATOR_LAYOUT( ch_analysis ) // Prepare all data needed by reporting for each pixelator step ch_input = channel.fromPath(params.input) diff --git a/subworkflows/local/pna/v2/meta.yml b/subworkflows/local/pna/v2/meta.yml index 05b0c203..5b35aa11 100644 --- a/subworkflows/local/pna/v2/meta.yml +++ b/subworkflows/local/pna/v2/meta.yml @@ -8,15 +8,15 @@ keywords: - fastq components: - cat/fastq - - pixelator/pna/amplicon - - pixelator/pna/demux - - pixelator/pna/collapse - - pixelator/pna/combine/collapse - - pixelator/pna/graph - - pixelator/pna/sample/calling - - pixelator/pna/denoise - - pixelator/pna/analysis - - pixelator/pna/layout + - pixelator/amplicon + - pixelator/demux + - pixelator/collapse + - pixelator/combine/collapse + - pixelator/graph + - pixelator/sample/calling + - pixelator/denoise + - pixelator/analysis + - pixelator/layout - experiment/summary - pna_generate_reports input: diff --git a/subworkflows/local/pna/v2/tests/main.nf.test.snap b/subworkflows/local/pna/v2/tests/main.nf.test.snap index a5547b77..c0c75b71 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v2/tests/main.nf.test.snap @@ -115,7 +115,7 @@ "pixelator/sample_calling/sample2.report.json" ] ], - "timestamp": "2026-05-13T14:43:57.33706874", + "timestamp": "2026-05-20T14:26:17.705500605", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/scripts/run_tests_parallel.sh b/tests/scripts/run_tests_parallel.sh index 3353cced..cded0677 100755 --- a/tests/scripts/run_tests_parallel.sh +++ b/tests/scripts/run_tests_parallel.sh @@ -12,7 +12,7 @@ nf-test test --profile test,docker $ARGS \ echo Running tests: PNA modules... nf-test test --profile test,docker $ARGS \ - modules/local/pixelator/single-cell-pna/ \ + modules/local/pixelator/ \ &> /tmp/pixelator_pna_modules_tests.txt \ && echo "Completed tests: PNA modules" & From ff40b1beba2ab16f365d3361bdab18d177b8ae2d Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 20 May 2026 14:50:11 +0200 Subject: [PATCH 72/90] Add back stable content variable --- tests/proxiome_v1.nf.test | 18 +++++++++---- tests/proxiome_v1.nf.test.snap | 46 +++++++++++++++++++--------------- tests/proxiome_v2.nf.test | 19 ++++++++++---- tests/proxiome_v2.nf.test.snap | 46 +++++++++++++++++++--------------- 4 files changed, 79 insertions(+), 50 deletions(-) diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index 0e125ad2..78e09036 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -16,8 +16,10 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files + folders in ${params.outdir}/ with a stable name + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = [] assertAll( { assert workflow.success}, @@ -27,7 +29,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), // All stable path name, with a relative path - stable_name, + stable_path, + // All files with stable contents + stable_content, ).match() } ) } @@ -44,14 +48,18 @@ nextflow_pipeline { } then { - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = [] assertAll( { assert workflow.success }, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // All stable path name, with a relative path - stable_name, + stable_path, + // All files with stable contents + stable_content, removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), ).match() } ) diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index d02e5546..2156da8d 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -94,6 +94,9 @@ "pixelator/logs/sample_2/sample_2.pixelator-layout.log", "pixelator/sample_1.pxl", "pixelator/sample_2.pxl" + ], + [ + ], { "CAT_FASTQ": { @@ -102,31 +105,31 @@ "EXPERIMENT_SUMMARY": { "experiment-summary": "0.10.1" }, - "PIXELATOR_LIST_OPTIONS": { + "PIXELATOR_AMPLICON": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_AMPLICON": { + "PIXELATOR_ANALYSIS": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_ANALYSIS": { + "PIXELATOR_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COLLAPSE": { + "PIXELATOR_COMBINE_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "PIXELATOR_DEMUX": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DEMUX": { + "PIXELATOR_DENOISE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DENOISE": { + "PIXELATOR_GRAPH": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_GRAPH": { + "PIXELATOR_LAYOUT": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_LAYOUT": { + "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" }, "Workflow": { @@ -134,7 +137,7 @@ } } ], - "timestamp": "2026-05-19T11:50:16.234033586", + "timestamp": "2026-05-20T14:48:04.425744385", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -150,31 +153,31 @@ "EXPERIMENT_SUMMARY": { "experiment-summary": "0.10.1" }, - "PIXELATOR_LIST_OPTIONS": { + "PIXELATOR_AMPLICON": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_AMPLICON": { + "PIXELATOR_ANALYSIS": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_ANALYSIS": { + "PIXELATOR_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COLLAPSE": { + "PIXELATOR_COMBINE_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "PIXELATOR_DEMUX": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DEMUX": { + "PIXELATOR_DENOISE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DENOISE": { + "PIXELATOR_GRAPH": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_GRAPH": { + "PIXELATOR_LAYOUT": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_LAYOUT": { + "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" }, "Workflow": { @@ -271,9 +274,12 @@ "pixelator/logs/sample_2/sample_2.pixelator-layout.log", "pixelator/sample_1.layout.pxl", "pixelator/sample_2.layout.pxl" + ], + [ + ] ], - "timestamp": "2026-05-19T11:48:56.493399385", + "timestamp": "2026-05-20T14:47:20.218323123", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index 838776b2..2db6d3d6 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -17,8 +17,10 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files + folders in ${params.outdir}/ with a stable name + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = [] assertAll( { assert workflow.success}, @@ -28,7 +30,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), // All stable path name, with a relative path - stable_name, + stable_path, + // All files with stable contents + stable_content, ).match() } ) } @@ -45,14 +49,19 @@ nextflow_pipeline { } then { - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files + folders in ${params.outdir}/ with a stable name + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = [] assertAll( { assert workflow.success }, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // All stable path name, with a relative path - stable_name, + stable_path, + // All files with stable contents + stable_content, removeNextflowVersion("$outputDir/pipeline_info/nf_core_pixelator_software_versions.yml"), ).match() } ) diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index f98dfec4..3bd0015d 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -131,6 +131,9 @@ "pixelator/sample_calling/sample2.dehashed.pxl", "pixelator/sample_calling/sample3.dehashed.pxl", "pixelator/sample_calling/sample4.dehashed.pxl" + ], + [ + ], { "CAT_FASTQ": { @@ -139,31 +142,31 @@ "EXPERIMENT_SUMMARY": { "experiment-summary": "0.10.1" }, - "PIXELATOR_LIST_OPTIONS": { + "PIXELATOR_AMPLICON": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_AMPLICON": { + "PIXELATOR_ANALYSIS": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_ANALYSIS": { + "PIXELATOR_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COLLAPSE": { + "PIXELATOR_COMBINE_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "PIXELATOR_DEMUX": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DEMUX": { + "PIXELATOR_DENOISE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DENOISE": { + "PIXELATOR_GRAPH": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_GRAPH": { + "PIXELATOR_LAYOUT": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_LAYOUT": { + "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" }, "Workflow": { @@ -171,7 +174,7 @@ } } ], - "timestamp": "2026-05-19T11:50:37.765871571", + "timestamp": "2026-05-20T14:40:47.828972504", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -187,31 +190,31 @@ "EXPERIMENT_SUMMARY": { "experiment-summary": "0.10.1" }, - "PIXELATOR_LIST_OPTIONS": { + "PIXELATOR_AMPLICON": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_AMPLICON": { + "PIXELATOR_ANALYSIS": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_ANALYSIS": { + "PIXELATOR_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COLLAPSE": { + "PIXELATOR_COMBINE_COLLAPSE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_COMBINE_COLLAPSE": { + "PIXELATOR_DEMUX": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DEMUX": { + "PIXELATOR_DENOISE": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_DENOISE": { + "PIXELATOR_GRAPH": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_GRAPH": { + "PIXELATOR_LAYOUT": { "pixelator": "0.26.0" }, - "PIXELATOR_PNA_LAYOUT": { + "PIXELATOR_LIST_OPTIONS": { "pixelator": "0.26.0" }, "Workflow": { @@ -355,9 +358,12 @@ "pixelator/sample_calling/sample4.dehashed.pxl", "pixelator/sample_calling/sample4.meta.json", "pixelator/sample_calling/sample4.report.json" + ], + [ + ] ], - "timestamp": "2026-05-19T11:49:07.544804495", + "timestamp": "2026-05-20T14:39:49.603104266", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 456cfa39cc42a7825568d64f79f8426133cdb62e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 10:15:06 +0200 Subject: [PATCH 73/90] Add missing new parameters to changelog --- CHANGELOG.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c7612f5e..0fa02055 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,12 +34,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------------------------------ | --------------------------- | -| `--leiden-iterations` | | -| `--min-component-size-in-refinement` | | -| `--min-component-size-to-prune` | | -| | `--edge_cycle-verification` | +| Old parameter | New parameter | +| ------------------------------------ | ----------------------------------------- | +| `--leiden-iterations` | | +| `--min-component-size-in-refinement` | | +| `--min-component-size-to-prune` | | +| | `--edge_cycle-verification` | +| | `save_pna_sample_calling_pixelfile` | +| | `pna_sample_calling_save_undetermined` | +| | `pna_sample_calling_remove_incompatible` | +| | `pna_sample_calling_confidence_threshold` | > [!NOTE] > Parameter has been **updated** if both old and new parameter information is present. From f02159496d83e9021b97d5b7d4713b2e54953341 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 10:15:22 +0200 Subject: [PATCH 74/90] Fix metromap --- docs/images/nf-core-pixelator-metromap.svg | 43 +++++++--------------- 1 file changed, 14 insertions(+), 29 deletions(-) diff --git a/docs/images/nf-core-pixelator-metromap.svg b/docs/images/nf-core-pixelator-metromap.svg index 94f5f6f3..90af051b 100644 --- a/docs/images/nf-core-pixelator-metromap.svg +++ b/docs/images/nf-core-pixelator-metromap.svg @@ -8,7 +8,7 @@ - + @@ -23,9 +23,9 @@ - + - + @@ -35,7 +35,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -84,7 +84,7 @@ - + @@ -95,31 +95,25 @@ - + - - - + + - - - + - - - - + + - - + @@ -258,16 +252,7 @@ - - - - - - - - - - + From fdf5f3ff7a4d1e938c66a4218668b48f6ac24890 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 10:44:45 +0200 Subject: [PATCH 75/90] Make --technology mandatory --- CHANGELOG.md | 1 + README.md | 1 + docs/usage.md | 6 +++--- nextflow.config | 2 +- nextflow_schema.json | 5 ++--- 5 files changed, 8 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0fa02055..8583692a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `--leiden-iterations` | | | `--min-component-size-in-refinement` | | | `--min-component-size-to-prune` | | +| | `--technology` | | | `--edge_cycle-verification` | | | `save_pna_sample_calling_pixelfile` | | | `pna_sample_calling_save_undetermined` | diff --git a/README.md b/README.md index 6fe9d573..f6dcb80f 100644 --- a/README.md +++ b/README.md @@ -83,6 +83,7 @@ Now, you can run the pipeline using: ```bash nextflow run nf-core/pixelator \ -profile , \ + --technology --input samplesheet.csv \ --outdir ``` diff --git a/docs/usage.md b/docs/usage.md index 4c7c6ff2..d35200d9 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -125,7 +125,7 @@ You can use following samplesheet: ```csv title="samplesheet.csv" sample,sample_alias,condition,design,panel,panel_file,fastq_1,fastq_2 -sample1,s1,control,pna-2,proxiome-immuno-155-v2,,fastq/sample1_R1.fq.gz,fastq/sample1_R2.fq.gz +sample1,s1,control,proxiome-v1,proxiome-v1-immuno-155-v1.1,,fastq/sample1_R1.fq.gz,fastq/sample1_R2.fq.gz ``` Using the `--input_basedir` option you can specify a different location that will be used to resolve relative paths. @@ -138,7 +138,7 @@ For example, using the same samplesheet as above, but with the samplesheet on th - sample1_R2.fq.gz ```shell -nextflow run nf-core/pixelator --input samplesheet.csv --input_basedir s3://my-company-data/experiment-1/ +nextflow run nf-core/pixelator --input samplesheet.csv --input_basedir s3://my-company-data/experiment-1/ --output ./resulst --technology proxiome-v1 ``` ### Design @@ -173,7 +173,7 @@ pixelator single-cell-pna --list-panels The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results -profile docker,cells_8k +nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results -profile docker,cells_8k --technology proxiome-v2 ``` This will launch the pipeline with the `docker` configuration profile, and resource configurations diff --git a/nextflow.config b/nextflow.config index 38e830ba..053d2454 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,7 +35,7 @@ params { save_pna_denoise_pixelfile = false save_pna_analysis_pixelfile = false - technology = "proxiome-v1" + technology = null // PNA amplicon pna_amplicon_mismatches = 0.1 diff --git a/nextflow_schema.json b/nextflow_schema.json index a3b6d885..485215f8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "outdir"], + "required": ["input", "outdir", "technology"], "properties": { "input": { "type": "string", @@ -497,8 +497,7 @@ "type": "string", "fa_icon": "fas fa-microchip", "description": "The technology used to process the samples", - "enum": ["proxiome-v1", "proxiome-v2", "hashed_samples", "nonhashed_samples"], - "default": "proxiome-v1" + "enum": ["proxiome-v1", "proxiome-v2", "hashed_samples", "nonhashed_samples"] } } }, From aa1149bdcd9b929a26ca879fba4e83e193487135 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 11:12:46 +0200 Subject: [PATCH 76/90] Rework test config files --- conf/test.config | 25 ------------- conf/test_proxiome_v1.config | 16 +++++++-- conf/test_proxiome_v2.config | 16 +++++++-- .../tests/main.nf.test.snap | 3 +- .../amplicon/tests/main.nf.test.snap | 3 +- .../analysis/tests/main.nf.test.snap | 3 +- .../collapse/tests/main.nf.test.snap | 6 ++-- .../combine_collapse/tests/main.nf.test.snap | 3 +- .../pixelator/demux/tests/main.nf.test.snap | 6 ++-- .../pixelator/denoise/tests/main.nf.test.snap | 3 +- .../pixelator/graph/tests/main.nf.test.snap | 3 +- .../pixelator/layout/tests/main.nf.test.snap | 3 +- .../sample_calling/tests/main.nf.test.snap | 3 +- nextflow.config | 1 + nextflow_schema.json | 6 ++++ subworkflows/local/pna/v1/nextflow.config | 5 --- subworkflows/local/pna/v1/tests/main.nf.test | 7 +++- .../local/pna/v1/tests/main.nf.test.snap | 3 +- subworkflows/local/pna/v2/nextflow.config | 5 --- subworkflows/local/pna/v2/tests/main.nf.test | 7 +++- .../local/pna/v2/tests/main.nf.test.snap | 3 +- tests/nextflow.config | 35 +++---------------- tests/proxiome_v1.nf.test | 12 +++++-- tests/proxiome_v2.nf.test | 20 +++++++++-- tests/proxiome_v2.nf.test.snap | 4 +-- 25 files changed, 107 insertions(+), 94 deletions(-) delete mode 100644 conf/test.config delete mode 100644 subworkflows/local/pna/v1/nextflow.config delete mode 100644 subworkflows/local/pna/v2/nextflow.config diff --git a/conf/test.config b/conf/test.config deleted file mode 100644 index 42cf329b..00000000 --- a/conf/test.config +++ /dev/null @@ -1,25 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Base Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Base configuration common to all test profiles ----------------------------------------------------------------------------------------- -*/ - - -// Base directory for nf-core/modules test data -params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' -params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pixelator/' - -process { - withName: '.*' { - cpus = 2 - memory = 3.GB - time = 2.h - } - - // Run a smaller experiment summary for testing - withName: EXPERIMENT_SUMMARY { - ext.args = '-P test_mode="TRUE"' - } -} diff --git a/conf/test_proxiome_v1.config b/conf/test_proxiome_v1.config index fb998abf..afe193a4 100644 --- a/conf/test_proxiome_v1.config +++ b/conf/test_proxiome_v1.config @@ -11,9 +11,6 @@ ---------------------------------------------------------------------------------------- */ -// Include testdata base path, resource allocations and process configuration -includeConfig 'test.config' - params { config_profile_name = 'Test profile for proxiome v1 data' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -28,3 +25,16 @@ params { technology = "proxiome-v1" save_all = true } + +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } + + // Run a smaller experiment summary for testing + withName: EXPERIMENT_SUMMARY { + ext.args = '-P test_mode="TRUE"' + } +} diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 56c5d589..23257b8c 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -11,9 +11,6 @@ ---------------------------------------------------------------------------------------- */ -// Include testdata base path, resource allocations and process configuration -includeConfig 'test.config' - params { config_profile_name = 'Test profile for proxiome v2 data' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -28,3 +25,16 @@ params { technology = "proxiome-v2" save_all = true } + +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } + + // Run a smaller experiment summary for testing + withName: EXPERIMENT_SUMMARY { + ext.args = '-P test_mode="TRUE"' + } +} diff --git a/modules/local/experiment_summary/tests/main.nf.test.snap b/modules/local/experiment_summary/tests/main.nf.test.snap index 81557181..4410fd25 100644 --- a/modules/local/experiment_summary/tests/main.nf.test.snap +++ b/modules/local/experiment_summary/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/experiment-summary.html" ], @@ -14,7 +15,7 @@ ] ] ], - "timestamp": "2026-05-13T13:53:08.409767489", + "timestamp": "2026-05-21T11:58:35.886952064", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/amplicon/tests/main.nf.test.snap index 4f4dd938..479969e7 100644 --- a/modules/local/pixelator/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/amplicon/tests/main.nf.test.snap @@ -126,6 +126,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/amplicon", "pixelator/amplicon/pool1.amplicon.fq.zst", @@ -143,7 +144,7 @@ ] ] ], - "timestamp": "2026-05-20T14:27:49.821596738", + "timestamp": "2026-05-21T11:56:54.148117208", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/analysis/tests/main.nf.test.snap b/modules/local/pixelator/analysis/tests/main.nf.test.snap index 2b0ea0ca..aa130c7b 100644 --- a/modules/local/pixelator/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/analysis/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/analysis", "pixelator/analysis/sample1.analysis.pxl", @@ -20,7 +21,7 @@ ] ] ], - "timestamp": "2026-05-20T14:28:25.911951216", + "timestamp": "2026-05-21T11:57:42.454900722", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/collapse/tests/main.nf.test.snap b/modules/local/pixelator/collapse/tests/main.nf.test.snap index 3027bca4..57a182ea 100644 --- a/modules/local/pixelator/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/collapse/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/collapse", "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", @@ -20,7 +21,7 @@ ] ] ], - "timestamp": "2026-05-20T14:28:49.824808507", + "timestamp": "2026-05-21T11:58:24.85769919", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -161,6 +162,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/collapse", "pixelator/collapse/pool1.collapse.m1.part_000.meta.json", @@ -175,7 +177,7 @@ ], null ], - "timestamp": "2026-05-13T13:53:27.172850517", + "timestamp": "2026-05-21T11:58:56.273822152", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap index 1b3dd56a..b2e75a61 100644 --- a/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/collapse", "pixelator/collapse/pool1.collapse.parquet", @@ -19,7 +20,7 @@ ] ] ], - "timestamp": "2026-05-20T14:29:29.978160031", + "timestamp": "2026-05-21T11:59:42.965992059", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/demux/tests/main.nf.test.snap b/modules/local/pixelator/demux/tests/main.nf.test.snap index e08d02ad..dba8dc77 100644 --- a/modules/local/pixelator/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/demux/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/demux", "pixelator/demux/pool1.demux.failed.fq.zst", @@ -23,7 +24,7 @@ ] ] ], - "timestamp": "2026-05-20T14:30:04.325516148", + "timestamp": "2026-05-21T12:00:37.132304324", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -209,6 +210,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/demux", "pixelator/demux/pool1.demux.failed.fq.zst", @@ -243,7 +245,7 @@ ] ] ], - "timestamp": "2026-05-20T14:30:29.692789975", + "timestamp": "2026-05-21T12:01:07.6787683", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/denoise/tests/main.nf.test.snap b/modules/local/pixelator/denoise/tests/main.nf.test.snap index 447a75f9..70b8cfa2 100644 --- a/modules/local/pixelator/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/denoise/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/denoise", "pixelator/denoise/sample1.meta.json", @@ -19,7 +20,7 @@ ] ] ], - "timestamp": "2026-05-20T14:30:51.886838398", + "timestamp": "2026-05-21T12:01:36.760255316", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/graph/tests/main.nf.test.snap b/modules/local/pixelator/graph/tests/main.nf.test.snap index 612d911f..98c4ff8f 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/graph/tests/main.nf.test.snap @@ -156,6 +156,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/graph", "pixelator/graph/pool1.graph.pxl", @@ -173,7 +174,7 @@ ] ] ], - "timestamp": "2026-05-20T14:31:17.955182089", + "timestamp": "2026-05-21T12:02:11.997776808", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/layout/tests/main.nf.test.snap b/modules/local/pixelator/layout/tests/main.nf.test.snap index 41951b62..cd2c7733 100644 --- a/modules/local/pixelator/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/layout/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/layout", "pixelator/layout/sample1.meta.json", @@ -20,7 +21,7 @@ ] ] ], - "timestamp": "2026-05-20T14:31:41.190244206", + "timestamp": "2026-05-21T12:02:56.888630957", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/local/pixelator/sample_calling/tests/main.nf.test.snap b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap index 0a7659b9..7d531009 100644 --- a/modules/local/pixelator/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 1, [ + "pipeline_info", "pixelator", "pixelator/logs", "pixelator/logs/pool1", @@ -20,7 +21,7 @@ ], null ], - "timestamp": "2026-05-18T16:07:43.50926016", + "timestamp": "2026-05-21T12:03:20.674454727", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/nextflow.config b/nextflow.config index 053d2454..cc2c2e51 100644 --- a/nextflow.config +++ b/nextflow.config @@ -116,6 +116,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') // Config options diff --git a/nextflow_schema.json b/nextflow_schema.json index 485215f8..4890f276 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -605,6 +605,12 @@ "default": "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/", "hidden": true }, + "modules_testdata_base_path": { + "type": "string", + "description": "Base path / URL for data used in the modules", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/", + "hidden": true + }, "trace_report_suffix": { "type": "string", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", diff --git a/subworkflows/local/pna/v1/nextflow.config b/subworkflows/local/pna/v1/nextflow.config deleted file mode 100644 index 47a2cd6f..00000000 --- a/subworkflows/local/pna/v1/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -// Include testdata base path, resource allocations and process configuration -includeConfig '../../../../conf/test.config' - -params.pna_demux_output_chunk_reads = "30K" -params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index 2b35a380..bd9f19da 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -2,13 +2,16 @@ nextflow_workflow { name "Test Workflow PIXELATOR_PNA_V1" script "../main.nf" - config "../nextflow.config" workflow "PIXELATOR_PNA_V1" + tag "subworkflows" tag "subworkflows_pixelator" tag "pixelator" tag "pixelator/pna" + def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) + def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String + test("Default parameters [design: proxiome-v1, panel: proxiome-v1-immuno-155-v1.1]") { when { @@ -16,6 +19,8 @@ nextflow_workflow { pna_graph_component_size_min_threshold = 100 skip_experiment_summary = true outdir = "$outputDir" + pna_demux_output_chunk_reads = "30K" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' } workflow { diff --git a/subworkflows/local/pna/v1/tests/main.nf.test.snap b/subworkflows/local/pna/v1/tests/main.nf.test.snap index a566050a..8078d9d0 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v1/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 19, [ + "pipeline_info", "pixelator", "pixelator/amplicon", "pixelator/amplicon/sample1.amplicon.fq.zst", @@ -92,7 +93,7 @@ "pixelator/logs/sample1.pixelator-layout.log" ] ], - "timestamp": "2026-05-20T14:22:55.637136331", + "timestamp": "2026-05-21T13:27:10.984127921", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/local/pna/v2/nextflow.config b/subworkflows/local/pna/v2/nextflow.config deleted file mode 100644 index 47a2cd6f..00000000 --- a/subworkflows/local/pna/v2/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -// Include testdata base path, resource allocations and process configuration -includeConfig '../../../../conf/test.config' - -params.pna_demux_output_chunk_reads = "30K" -params.input = params.pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index cc0dbc8f..d8ac6aac 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -2,13 +2,16 @@ nextflow_workflow { name "Test Workflow PIXELATOR_PNA_V2" script "../main.nf" - config "../nextflow.config" workflow "PIXELATOR_PNA_V2" + tag "subworkflows" tag "subworkflows_pixelator" tag "pixelator" tag "pixelator/pna" + def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) + def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String + test("Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v1.0]") { when { @@ -16,6 +19,8 @@ nextflow_workflow { pna_graph_component_size_min_threshold = 100 skip_experiment_summary = true outdir = "$outputDir" + pna_demux_output_chunk_reads = "30K" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' } workflow { diff --git a/subworkflows/local/pna/v2/tests/main.nf.test.snap b/subworkflows/local/pna/v2/tests/main.nf.test.snap index c0c75b71..9ec2f968 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test.snap +++ b/subworkflows/local/pna/v2/tests/main.nf.test.snap @@ -3,6 +3,7 @@ "content": [ 23, [ + "pipeline_info", "pixelator", "pixelator/amplicon", "pixelator/amplicon/pool1.amplicon.fq.zst", @@ -115,7 +116,7 @@ "pixelator/sample_calling/sample2.report.json" ] ], - "timestamp": "2026-05-20T14:26:17.705500605", + "timestamp": "2026-05-21T13:22:23.285610507", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/nextflow.config b/tests/nextflow.config index 1171b445..3dd26c68 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,35 +4,10 @@ ======================================================================================== */ -// Include testdata base path, resource allocations and process configuration -includeConfig '../conf/test.config' - -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners - -params.outdir = 'results' -params.modules_testdata_base_path = params.modules_testdata_base_path -params.pipelines_testdata_base_path = params.pipelines_testdata_base_path - - -validation { - ignoreParams = ['modules_testdata_base_path', 'pipelines_testdata_base_path'] -} - -// Impose same minimum Nextflow version as the pipeline for testing -manifest { - nextflowVersion = '!>=23.10.4' +params { + pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" + modules_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" + outdir = 'results' } -// Disable all Nextflow reporting options -timeline { - enabled = false -} -report { - enabled = false -} -trace { - enabled = false -} -dag { - enabled = false -} +aws.client.anonymous = true // fixes S3 access issues on self-hosted runners diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index 78e09036..2e3dd44f 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -2,16 +2,24 @@ nextflow_pipeline { name "Test PNA pipeline V1" script "../main.nf" - config "conf/test_proxiome_v1.config" tag "pixelator" tag "pixelator/pna" + def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) + def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String + test("Params: all") { when { params { - outdir = "$outputDir" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' + input_basedir = pipelines_testdata_base_path + "/testdata/pna/" + outdir = "$outputDir" + pna_graph_component_size_min_threshold = 100 + skip_experiment_summary = false + save_all = true + technology = "proxiome-v1" } } diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index 2db6d3d6..ac5bf564 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -2,17 +2,25 @@ nextflow_pipeline { name "Test PNA pipeline V2" script "../main.nf" - config "conf/test_proxiome_v2.config" tag "pixelator" tag "pixelator/pna" tag "smoke_test" + def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) + def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String + test("Params: all") { when { params { - outdir = "$outputDir" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' + input_basedir = pipelines_testdata_base_path + "/testdata/pna/" + outdir = "$outputDir" + pna_graph_component_size_min_threshold = 100 + skip_experiment_summary = false + save_all = true + technology = "proxiome-v2" } } @@ -44,7 +52,13 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' + input_basedir = pipelines_testdata_base_path + "/testdata/pna/" + outdir = "$outputDir" + pna_graph_component_size_min_threshold = 100 + skip_experiment_summary = false + save_all = true + technology = "proxiome-v2" } } diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 3bd0015d..2f9e63f8 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -174,7 +174,7 @@ } } ], - "timestamp": "2026-05-20T14:40:47.828972504", + "timestamp": "2026-05-21T11:48:37.212684532", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -363,7 +363,7 @@ ] ], - "timestamp": "2026-05-20T14:39:49.603104266", + "timestamp": "2026-05-21T11:47:38.637710599", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From d2dc532e876f7f14e227fb1f6397206732f4e4c8 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 13:42:52 +0200 Subject: [PATCH 77/90] Fix test profile in convenience scripts The test profile is defined in the nf-test.config --- tests/scripts/run_smoke_tests.sh | 2 +- tests/scripts/run_tests_parallel.sh | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/scripts/run_smoke_tests.sh b/tests/scripts/run_smoke_tests.sh index 8b598603..6eed9c67 100644 --- a/tests/scripts/run_smoke_tests.sh +++ b/tests/scripts/run_smoke_tests.sh @@ -4,4 +4,4 @@ ARGS=$@ -nf-test test --profile test,docker $ARGS --tag="smoke_test" +nf-test test --profile=+docker $ARGS --tag="smoke_test" diff --git a/tests/scripts/run_tests_parallel.sh b/tests/scripts/run_tests_parallel.sh index cded0677..fd2e9e1a 100755 --- a/tests/scripts/run_tests_parallel.sh +++ b/tests/scripts/run_tests_parallel.sh @@ -5,31 +5,31 @@ ARGS=$@ echo Running tests: experiment summary... -nf-test test --profile test,docker $ARGS \ +nf-test test --profile=+docker $ARGS \ modules/local/experiment_summary/ \ &> /tmp/pixelator_es_tests.txt \ && echo "Completed tests: experiment summary" & echo Running tests: PNA modules... -nf-test test --profile test,docker $ARGS \ +nf-test test --profile=+docker $ARGS \ modules/local/pixelator/ \ &> /tmp/pixelator_pna_modules_tests.txt \ && echo "Completed tests: PNA modules" & echo Running tests: subworkflows... -nf-test test --profile test,docker $ARGS \ +nf-test test --profile=+docker $ARGS \ subworkflows/ \ &> /tmp/pixelator_subworkflow_tests.txt \ && echo "Completed tests: subworkflows" & echo Running tests: PNA pipeline V1... -nf-test test --profile test,docker $ARGS \ +nf-test test --profile=+docker $ARGS \ tests/proxiome_v1.nf.test \ &> /tmp/pixelator_pna_pipeline_v1_tests.txt \ && echo "Completed tests: PNA pipeline" & echo Running tests: PNA pipeline V2... -nf-test test --profile test,docker $ARGS \ +nf-test test --profile=+docker $ARGS \ tests/proxiome_v2.nf.test \ &> /tmp/pixelator_pna_pipeline_v2_tests.txt \ && echo "Completed tests: PNA pipeline" & From bc570b36fdfd863265a529f7afad0debaa2b6570 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 13:53:30 +0200 Subject: [PATCH 78/90] Make it possible to override test data base path from env --- docs/CONTRIBUTING.md | 8 ++++++++ nextflow.config | 2 +- tests/nextflow.config | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index f17f4c0a..4cca3660 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -101,6 +101,14 @@ GitHub Actions runs the pipeline on this data to ensure it runs through and exit If there are any failures then the automated tests fail. These tests are run with the latest available version of Nextflow and the minimum required version specified in the pipeline code. +#### Test data + +By default, test data is downloaded from +https://github.com/nf-core/test-datasets/tree/pixelator. If one desires to use +local data instead, this can be overriden either with the +`pipelines_testdata_base_path` parameter or with the `NFT_TESTDATA_BASE_PATH` +environment variable. + ### Patch release > [!WARNING] diff --git a/nextflow.config b/nextflow.config index cc2c2e51..b2327638 100644 --- a/nextflow.config +++ b/nextflow.config @@ -115,7 +115,7 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/' + pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: 'https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/' modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') diff --git a/tests/nextflow.config b/tests/nextflow.config index 3dd26c68..1e12f8a5 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -5,7 +5,7 @@ */ params { - pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" + pipelines_testdata_base_path = System.getenv('NFT_TESTDATA_BASE_PATH') ?: "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/" modules_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" outdir = 'results' } From 675b398a3bc62682f368afe12e18eb7f70925cfb Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:08:56 +0200 Subject: [PATCH 79/90] Point test and test_full configs to proxiome_v2 --- conf/test.config | 14 ++++++++++++++ conf/test_full.config | 2 +- nextflow.config | 2 +- 3 files changed, 16 insertions(+), 2 deletions(-) create mode 100644 conf/test.config diff --git a/conf/test.config b/conf/test.config new file mode 100644 index 00000000..25fdd474 --- /dev/null +++ b/conf/test.config @@ -0,0 +1,14 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test + for the pna pipline + + Use as follows: + nextflow run nf-core/pixelator -profile test_pna, --outdir + +---------------------------------------------------------------------------------------- +*/ + +includeConfig 'test_proxiome_v2.config' diff --git a/conf/test_full.config b/conf/test_full.config index 6bfdf1ea..25fdd474 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -11,4 +11,4 @@ ---------------------------------------------------------------------------------------- */ -includeConfig 'test_proxiome_v1.config' +includeConfig 'test_proxiome_v2.config' diff --git a/nextflow.config b/nextflow.config index b2327638..9212c8df 100644 --- a/nextflow.config +++ b/nextflow.config @@ -258,7 +258,7 @@ profiles { } test { - includeConfig 'conf/test_proxiome_v1.config' + includeConfig 'conf/test.config' } test_proxiome_v1 { From 54ad612beb21645d207b56077dc4eb1ad00c2b7b Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:13:50 +0200 Subject: [PATCH 80/90] Fix typo in test documentation --- conf/test.config | 2 +- conf/test_full.config | 2 +- conf/test_proxiome_v2.config | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index 25fdd474..4cfa08af 100644 --- a/conf/test.config +++ b/conf/test.config @@ -6,7 +6,7 @@ for the pna pipline Use as follows: - nextflow run nf-core/pixelator -profile test_pna, --outdir + nextflow run nf-core/pixelator -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 25fdd474..9c42b7cb 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -6,7 +6,7 @@ for the pna pipline Use as follows: - nextflow run nf-core/pixelator -profile test_pna, --outdir + nextflow run nf-core/pixelator -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_proxiome_v2.config b/conf/test_proxiome_v2.config index 23257b8c..7273a4df 100644 --- a/conf/test_proxiome_v2.config +++ b/conf/test_proxiome_v2.config @@ -6,7 +6,7 @@ for the pna pipline Use as follows: - nextflow run nf-core/pixelator -profile test_proxiome_v1, --outdir + nextflow run nf-core/pixelator -profile test_proxiome_v2, --outdir ---------------------------------------------------------------------------------------- */ From b9f5ad70b54f0f76a61e5ddb08ff3e2a98b1d791 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:15:13 +0200 Subject: [PATCH 81/90] Regenerate ro-crate --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 28a4414f..7963e0fc 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2026-05-19T08:43:42+00:00", - "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz\n```\n\n> [!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\n> [!WARNING]\n> Panel and design names have been completely renamed in pixelator 0.26\n> (nf-core/pixelator 4.0 and above). Refer to the pixelator\n> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0)\n> for more details.\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", + "description": "

    \n \n \n \"nf-core/pixelator\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/pixelator)\n[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the\nProximity Network (PNA) assay. It takes a samplesheet as input and will process your data\nusing `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.\n\n![](./docs/images/nf-core-pixelator-metromap.svg)\n\nThe pipeline will run the following steps:\n\n1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))\n2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))\n3. Derive original molecules to use as edge list downstream by error correcting, and counting input amplicons ([`pixelator single-cell-pna collapse`](https://github.com/PixelgenTechnologies/pixelator))\n4. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-pna graph`](https://github.com/PixelgenTechnologies/pixelator))\n5. _(Conditional; only for PNA hashed data)_ Assign components to samples in pooled experiments ([`pixelator single-cell-pna sample-calling`](https://github.com/PixelgenTechnologies/pixelator))\n6. Denoise the cell graphs ([`pixelator single-cell-pna denoise`](https://github.com/PixelgenTechnologies/pixelator))\n7. Analyze the spatial information in the cell graphs ([`pixelator single-cell-pna analysis`](https://github.com/PixelgenTechnologies/pixelator))\n8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))\n9. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)\n\n> [!NOTE]\n> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),\n> which is the last version to support that data type.\n\n> [!WARNING]\n> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.\n> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable\n> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows (the exact values you need to input depend on the design and panel you are using - please see [https://nf-co.re/pixelator/usage](https://nf-co.re/pixelator/usage) for more details).\nFor hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:\n\n`samplesheet.csv`:\n\n```csv\npool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2\npool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz\n```\n\n> [!NOTE]\n> For an example with non-hashed PNA data (Proxiome kit v1), see [Proxiome v1 samplesheet](../assets/samplesheet_proxiome_v1.csv)\n\n> [!WARNING]\n> Panel and design names have been completely renamed in pixelator 0.26\n> (nf-core/pixelator 4.0 and above). Refer to the pixelator\n> [changelog](https://github.com/PixelgenTechnologies/pixelator/releases/tag/v0.26.0)\n> for more details.\n\nEach row represents a sample and gives the design, a panel file and the input fastq files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/pixelator \\\n -profile , \\\n --technology \n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> This version of the pipeline does not support conda environments, due to issues with upstream dependencies.\n> This means you cannot use the `conda` and `mamba` profiles. Please use `docker` or `singularity` instead.\n> We hope to add support for conda environments in the future.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pixelator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pixelator/output).\n\n## Credits\n\nnf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:\n\n- Florian De Temmerman\n- Johan Dahlberg\n- Alvaro Martinez Barrio\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pixelator` channel](https://nfcore.slack.com/channels/pixelator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can cite the Proximity Network Technology as follows:\n\n> **Single-Cell Protein Interactomes by the Proximity Network Assay.**\n>\n> Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franz\u00e9n, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson\n>\n> _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)\n", "hasPart": [ { "@id": "main.nf" From 3159a3b9e38791d5edb1e0123e4d3349f0e0deb7 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:15:55 +0200 Subject: [PATCH 82/90] Fix nf-core config --- .nf-core.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index c3ebd280..13526eda 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -3,7 +3,6 @@ lint: - assets/multiqc_config.yml - conf/igenomes.config - conf/igenomes_ignored.config - - conf/test.config - tests/default.nf.test files_unchanged: - assets/nf-core-pixelator_logo_light.png From f1bade7edbc4c671288ceccd252ffc773c1d1c5f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:18:39 +0200 Subject: [PATCH 83/90] Fix example samplesheet proxiome v2 --- assets/example_samplesheet_proxiome_v2.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/example_samplesheet_proxiome_v2.csv b/assets/example_samplesheet_proxiome_v2.csv index 54d579a4..7e721723 100644 --- a/assets/example_samplesheet_proxiome_v2.csv +++ b/assets/example_samplesheet_proxiome_v2.csv @@ -1,3 +1,3 @@ pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2 -pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample1_R1_001.fastq.gz,sample1_R2_001.fastq.gz -pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,sample2_R1_001.fastq.gz,sample2_R2_001.fastq.gz +pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz +pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz From 8dd501fb89724ecb2c56bda64dc8f907fc999f86 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:19:03 +0200 Subject: [PATCH 84/90] Fix linting --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 4890f276..38aa0806 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -608,7 +608,7 @@ "modules_testdata_base_path": { "type": "string", "description": "Base path / URL for data used in the modules", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/", "hidden": true }, "trace_report_suffix": { From aaf012dc274e8418421bc4ece755025e3a7e2e1e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 21 May 2026 14:43:07 +0200 Subject: [PATCH 85/90] Add missing test params --- tests/proxiome_v1.nf.test | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index 2e3dd44f..f6c70851 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -51,7 +51,13 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' + input_basedir = pipelines_testdata_base_path + "/testdata/pna/" + outdir = "$outputDir" + pna_graph_component_size_min_threshold = 100 + skip_experiment_summary = false + save_all = true + technology = "proxiome-v1" } } From 0b3f6de593fafb7352451d9802939ed19b1c2f8b Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 22 May 2026 08:51:16 +0200 Subject: [PATCH 86/90] Remove tag files --- modules/local/pixelator/amplicon/tests/tags.yml | 2 -- modules/local/pixelator/analysis/tests/tags.yml | 2 -- modules/local/pixelator/collapse/tests/tags.yml | 2 -- modules/local/pixelator/combine_collapse/tests/tags.yml | 2 -- modules/local/pixelator/demux/tests/tags.yml | 2 -- modules/local/pixelator/graph/tests/tags.yml | 2 -- subworkflows/local/pna/v1/tests/tags.yml | 2 -- subworkflows/local/pna/v2/tests/tags.yml | 2 -- 8 files changed, 16 deletions(-) delete mode 100644 modules/local/pixelator/amplicon/tests/tags.yml delete mode 100644 modules/local/pixelator/analysis/tests/tags.yml delete mode 100644 modules/local/pixelator/collapse/tests/tags.yml delete mode 100644 modules/local/pixelator/combine_collapse/tests/tags.yml delete mode 100644 modules/local/pixelator/demux/tests/tags.yml delete mode 100644 modules/local/pixelator/graph/tests/tags.yml delete mode 100644 subworkflows/local/pna/v1/tests/tags.yml delete mode 100644 subworkflows/local/pna/v2/tests/tags.yml diff --git a/modules/local/pixelator/amplicon/tests/tags.yml b/modules/local/pixelator/amplicon/tests/tags.yml deleted file mode 100644 index 951d203c..00000000 --- a/modules/local/pixelator/amplicon/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/amplicon: - - modules/local/pixelator/amplicon/** diff --git a/modules/local/pixelator/analysis/tests/tags.yml b/modules/local/pixelator/analysis/tests/tags.yml deleted file mode 100644 index 7b55a59e..00000000 --- a/modules/local/pixelator/analysis/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/analysis: - - modules/local/pixelator/analysis/** diff --git a/modules/local/pixelator/collapse/tests/tags.yml b/modules/local/pixelator/collapse/tests/tags.yml deleted file mode 100644 index 44eaf569..00000000 --- a/modules/local/pixelator/collapse/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/collapse: - - modules/local/pixelator/collapse/** diff --git a/modules/local/pixelator/combine_collapse/tests/tags.yml b/modules/local/pixelator/combine_collapse/tests/tags.yml deleted file mode 100644 index dfb7bcad..00000000 --- a/modules/local/pixelator/combine_collapse/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/combine_collapse: - - modules/local/pixelator/combine_collapse/** diff --git a/modules/local/pixelator/demux/tests/tags.yml b/modules/local/pixelator/demux/tests/tags.yml deleted file mode 100644 index 437d9ed8..00000000 --- a/modules/local/pixelator/demux/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/demux: - - modules/local/pixelator/demux/** diff --git a/modules/local/pixelator/graph/tests/tags.yml b/modules/local/pixelator/graph/tests/tags.yml deleted file mode 100644 index 5688ce02..00000000 --- a/modules/local/pixelator/graph/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/graph: - - modules/local/pixelator/graph/** diff --git a/subworkflows/local/pna/v1/tests/tags.yml b/subworkflows/local/pna/v1/tests/tags.yml deleted file mode 100644 index 0c395141..00000000 --- a/subworkflows/local/pna/v1/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/pna: - - subworkflows/local/pna/** diff --git a/subworkflows/local/pna/v2/tests/tags.yml b/subworkflows/local/pna/v2/tests/tags.yml deleted file mode 100644 index 0c395141..00000000 --- a/subworkflows/local/pna/v2/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pixelator/pna: - - subworkflows/local/pna/** From 4e761bed0fe13a98534156a8b1603e63c9f3605e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 22 May 2026 09:02:43 +0200 Subject: [PATCH 87/90] Document test utility scripts in contributing guidelines --- docs/CONTRIBUTING.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 4cca3660..0428ee2d 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -77,6 +77,16 @@ Update the snapshots with the following command: nf-test test --tag test --profile +docker --verbose --update-snapshots ``` +Some tests can take quite long to run. To solve this we provide two utility scripts: + +- `run_smoke_tests.sh`: this runs all tests tagged with `smoke_test`. This is a good way to quickly + make sure nothing is broken after making some changes. +- `run_tests_parallel.sh`: this runs all the tests in parallel using on 5 different threads. + This is useful to update all the snapshots at once before making a PR. + +Both scripts take the same parameters `nf-test` does, e.g. run +`bash tests/scripts/run_tests_parallel.sh --update-snapshots` to update all snapshots. + When you create a pull request with changes, GitHub Actions will run automatic tests. Pull requests are typically reviewed when these tests are passing. From d778509226ac7e64846aa968173891df7530eb2a Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 22 May 2026 09:15:37 +0200 Subject: [PATCH 88/90] Use profiles to spec test inputs --- subworkflows/local/pna/v1/tests/main.nf.test | 6 +----- subworkflows/local/pna/v2/tests/main.nf.test | 6 +----- tests/proxiome_v1.nf.test | 16 +--------------- tests/proxiome_v2.nf.test | 13 +------------ 4 files changed, 4 insertions(+), 37 deletions(-) diff --git a/subworkflows/local/pna/v1/tests/main.nf.test b/subworkflows/local/pna/v1/tests/main.nf.test index bd9f19da..660477a1 100644 --- a/subworkflows/local/pna/v1/tests/main.nf.test +++ b/subworkflows/local/pna/v1/tests/main.nf.test @@ -3,24 +3,20 @@ nextflow_workflow { name "Test Workflow PIXELATOR_PNA_V1" script "../main.nf" workflow "PIXELATOR_PNA_V1" + profile "test_proxiome_v1" tag "subworkflows" tag "subworkflows_pixelator" tag "pixelator" tag "pixelator/pna" - def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) - def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String - test("Default parameters [design: proxiome-v1, panel: proxiome-v1-immuno-155-v1.1]") { when { params { - pna_graph_component_size_min_threshold = 100 skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' } workflow { diff --git a/subworkflows/local/pna/v2/tests/main.nf.test b/subworkflows/local/pna/v2/tests/main.nf.test index d8ac6aac..59df3a91 100644 --- a/subworkflows/local/pna/v2/tests/main.nf.test +++ b/subworkflows/local/pna/v2/tests/main.nf.test @@ -3,24 +3,20 @@ nextflow_workflow { name "Test Workflow PIXELATOR_PNA_V2" script "../main.nf" workflow "PIXELATOR_PNA_V2" + profile "test_proxiome_v2" tag "subworkflows" tag "subworkflows_pixelator" tag "pixelator" tag "pixelator/pna" - def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) - def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String - test("Default parameters [design: proxiome-v2, panel: proxiome-v2-immuno-155-v1.0]") { when { params { - pna_graph_component_size_min_threshold = 100 skip_experiment_summary = true outdir = "$outputDir" pna_demux_output_chunk_reads = "30K" - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' } workflow { diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index f6c70851..cfa71306 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -2,24 +2,16 @@ nextflow_pipeline { name "Test PNA pipeline V1" script "../main.nf" + profile "test_proxiome_v1" tag "pixelator" tag "pixelator/pna" - def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) - def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String - test("Params: all") { when { params { - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' - input_basedir = pipelines_testdata_base_path + "/testdata/pna/" outdir = "$outputDir" - pna_graph_component_size_min_threshold = 100 - skip_experiment_summary = false - save_all = true - technology = "proxiome-v1" } } @@ -51,13 +43,7 @@ nextflow_pipeline { when { params { - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v1.csv' - input_basedir = pipelines_testdata_base_path + "/testdata/pna/" outdir = "$outputDir" - pna_graph_component_size_min_threshold = 100 - skip_experiment_summary = false - save_all = true - technology = "proxiome-v1" } } diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index ac5bf564..83c2572c 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -2,6 +2,7 @@ nextflow_pipeline { name "Test PNA pipeline V2" script "../main.nf" + profile "test_proxiome_v2" tag "pixelator" tag "pixelator/pna" @@ -14,13 +15,7 @@ nextflow_pipeline { when { params { - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' - input_basedir = pipelines_testdata_base_path + "/testdata/pna/" outdir = "$outputDir" - pna_graph_component_size_min_threshold = 100 - skip_experiment_summary = false - save_all = true - technology = "proxiome-v2" } } @@ -52,13 +47,7 @@ nextflow_pipeline { when { params { - input = pipelines_testdata_base_path + '/samplesheet/pna/samplesheet_proxiome_v2.csv' - input_basedir = pipelines_testdata_base_path + "/testdata/pna/" outdir = "$outputDir" - pna_graph_component_size_min_threshold = 100 - skip_experiment_summary = false - save_all = true - technology = "proxiome-v2" } } From 542e6d4986452f2d53161e6dcdb50af721de8314 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 22 May 2026 11:49:40 +0200 Subject: [PATCH 89/90] Add meta.json to stable content --- tests/proxiome_v1.nf.test | 8 +++--- tests/proxiome_v1.nf.test.snap | 30 +++++++++++++++++--- tests/proxiome_v2.nf.test | 8 +++--- tests/proxiome_v2.nf.test.snap | 50 +++++++++++++++++++++++++++++++--- 4 files changed, 80 insertions(+), 16 deletions(-) diff --git a/tests/proxiome_v1.nf.test b/tests/proxiome_v1.nf.test index cfa71306..b119b433 100644 --- a/tests/proxiome_v1.nf.test +++ b/tests/proxiome_v1.nf.test @@ -11,7 +11,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -19,7 +19,7 @@ nextflow_pipeline { // stable_path: All files + folders in ${params.outdir}/ with a stable name def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = [] + def stable_content = getAllFilesFromDir(params.outdir, include: ['**/*.meta.json'], ignore: ['pixelator/collapse/*']) assertAll( { assert workflow.success}, @@ -43,14 +43,14 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } then { def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = [] + def stable_content = getAllFilesFromDir(params.outdir, include: ['**/*.meta.json'], ignore: ['pixelator/collapse/*']) assertAll( { assert workflow.success }, { assert snapshot( diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index 2156da8d..04cc95e3 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -96,7 +96,18 @@ "pixelator/sample_2.pxl" ], [ - + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample_2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ], { "CAT_FASTQ": { @@ -137,7 +148,7 @@ } } ], - "timestamp": "2026-05-20T14:48:04.425744385", + "timestamp": "2026-05-22T14:45:44.906565007", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -276,10 +287,21 @@ "pixelator/sample_2.layout.pxl" ], [ - + "sample_1.meta.json:md5,5e252f7062a4b444c53b1bfeb07ba9db", + "sample_2.meta.json:md5,5e252f7062a4b444c53b1bfeb07ba9db", + "sample_1.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "sample_2.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "sample_1.meta.json:md5,6ca7d2d473fee8a3ab667835f4057916", + "sample_2.meta.json:md5,e0b756a91edb80e878baa6862b2c3c6d", + "sample_1.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "sample_2.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "sample_1.meta.json:md5,9499ef2af613d6fa5cba5c91a443c726", + "sample_2.meta.json:md5,d73dc0fcfaaac01957e4611c89ef3dec", + "sample_1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", + "sample_2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3" ] ], - "timestamp": "2026-05-20T14:47:20.218323123", + "timestamp": "2026-05-22T14:44:59.750008727", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index 83c2572c..2a873767 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -15,7 +15,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -23,7 +23,7 @@ nextflow_pipeline { // stable_path: All files + folders in ${params.outdir}/ with a stable name def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = [] + def stable_content = getAllFilesFromDir(params.outdir, include: ['**/*.meta.json'], ignore: ['pixelator/collapse/*']) assertAll( { assert workflow.success}, @@ -47,7 +47,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -55,7 +55,7 @@ nextflow_pipeline { // stable_path: All files + folders in ${params.outdir}/ with a stable name def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = [] + def stable_content = getAllFilesFromDir(params.outdir, include: ['**/*.meta.json'], ignore: ['pixelator/collapse/*']) assertAll( { assert workflow.success }, { assert snapshot( diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 2f9e63f8..13270a4a 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -133,7 +133,26 @@ "pixelator/sample_calling/sample4.dehashed.pxl" ], [ - + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample2.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample3.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "sample4.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool1.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "pool2.sample_calling.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e" ], { "CAT_FASTQ": { @@ -174,7 +193,7 @@ } } ], - "timestamp": "2026-05-21T11:48:37.212684532", + "timestamp": "2026-05-22T14:44:24.873076953", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -360,10 +379,33 @@ "pixelator/sample_calling/sample4.report.json" ], [ - + "pool1.meta.json:md5,41c228a0f862dd47e6b4b66b001cc44b", + "pool2.meta.json:md5,41c228a0f862dd47e6b4b66b001cc44b", + "sample1.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "sample2.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "sample3.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "sample4.meta.json:md5,2a6eaa66228775591525f74416f0b87f", + "pool1.meta.json:md5,84596e67700975fd7518a0fdeedf3168", + "pool2.meta.json:md5,84596e67700975fd7518a0fdeedf3168", + "sample1.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "sample2.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "sample3.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "sample4.meta.json:md5,d0728a1efc25964039497c7bc22cdc35", + "pool1.meta.json:md5,481df097c7b214be07def5d68f04e79d", + "pool2.meta.json:md5,481df097c7b214be07def5d68f04e79d", + "sample1.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", + "sample2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", + "sample3.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", + "sample4.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3", + "pool1_undetermined.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", + "pool2_undetermined.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", + "sample1.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", + "sample2.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", + "sample3.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7", + "sample4.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7" ] ], - "timestamp": "2026-05-21T11:47:38.637710599", + "timestamp": "2026-05-22T14:43:17.238109494", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From fc4b31420b3b146c636e13bfaef3ee06f675ccfe Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 22 May 2026 15:13:47 +0200 Subject: [PATCH 90/90] Remove leftover test config --- tests/proxiome_v2.nf.test | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/proxiome_v2.nf.test b/tests/proxiome_v2.nf.test index 2a873767..7d42fdf6 100644 --- a/tests/proxiome_v2.nf.test +++ b/tests/proxiome_v2.nf.test @@ -8,9 +8,6 @@ nextflow_pipeline { tag "pixelator/pna" tag "smoke_test" - def test_config = new ConfigSlurper().parse(new File("tests/nextflow.config").toURI().toURL()) - def pipelines_testdata_base_path = test_config.params.pipelines_testdata_base_path as String - test("Params: all") { when {