From 106319f9f1936633bbb821dbf8ee6b45c1024fbf Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Fri, 29 May 2026 15:58:02 +0200 Subject: [PATCH 1/6] Bump version to 4.2.0dev --- .nf-core.yml | 2 +- CHANGELOG.md | 2 ++ nextflow.config | 2 +- ro-crate-metadata.json | 18 +++++++++--------- tests/proxiome_v1.nf.test.snap | 4 ++-- tests/proxiome_v2.nf.test.snap | 4 ++-- 6 files changed, 17 insertions(+), 15 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index b6b6ee86..fe2ae4d6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -24,4 +24,4 @@ template: - fastqc - multiqc - igenomes - version: 4.1.1 + version: 4.2.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 92812783..44f1cc99 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). +## [[4.2.0dev](https://github.com/nf-core/pixelator/releases/tag/4.2.0)] - 2026-MM-DD + ## [[4.1.1](https://github.com/nf-core/pixelator/releases/tag/4.1.1)] - 2026-05-29 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index eabdcf5b..aab39cd9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.1.1' + version = '4.2.0dev' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8be93786..203e5807 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-05-29T12:26:37+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-05-29T13:57:42+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-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,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/example_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": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#00706bd6-3b40-441b-b58f-1612b1f4c14c" + "@id": "#b08e9a66-f8b8-4587-9a7e-10048983d129" } ], "name": "nf-core/pixelator" @@ -143,7 +143,7 @@ } ], "dateCreated": "", - "dateModified": "2026-05-29T14:26:37Z", + "dateModified": "2026-05-29T15:57:42Z", "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/4.1.1/" + "https://nf-co.re/pixelator/dev/" ], "version": [ - "4.1.1" + "4.2.0dev" ] }, { @@ -193,11 +193,11 @@ "version": "!>=25.10.4" }, { - "@id": "#00706bd6-3b40-441b-b58f-1612b1f4c14c", + "@id": "#b08e9a66-f8b8-4587-9a7e-10048983d129", "@type": "TestSuite", "instance": [ { - "@id": "#44382bdc-2766-47e3-a6ad-4b279f74cdea" + "@id": "#1ea56774-5744-4332-bf43-225123fa4115" } ], "mainEntity": { @@ -206,7 +206,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#44382bdc-2766-47e3-a6ad-4b279f74cdea", + "@id": "#1ea56774-5744-4332-bf43-225123fa4115", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index ed943f2c..af2fdada 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -144,7 +144,7 @@ "pixelator": "0.27.2" }, "Workflow": { - "nf-core/pixelator": "v4.1.1" + "nf-core/pixelator": "v4.2.0dev" } } ], @@ -192,7 +192,7 @@ "pixelator": "0.27.2" }, "Workflow": { - "nf-core/pixelator": "v4.1.1" + "nf-core/pixelator": "v4.2.0dev" } }, [ diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 04b8989c..b36dd271 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -181,7 +181,7 @@ "pixelator": "0.27.2" }, "Workflow": { - "nf-core/pixelator": "v4.1.1" + "nf-core/pixelator": "v4.2.0dev" } } ], @@ -229,7 +229,7 @@ "pixelator": "0.27.2" }, "Workflow": { - "nf-core/pixelator": "v4.1.1" + "nf-core/pixelator": "v4.2.0dev" } }, [ From baa3ff92d71b025770b539b1f02eb66046d6aa52 Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Wed, 3 Jun 2026 16:49:07 +0000 Subject: [PATCH 2/6] Update pixelator to 0.28.0 --- CHANGELOG.md | 10 ++++++ modules/local/pixelator/amplicon/main.nf | 4 +-- .../amplicon/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/analysis/main.nf | 4 +-- .../analysis/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/collapse/main.nf | 4 +-- .../collapse/tests/main.nf.test.snap | 6 ++-- .../local/pixelator/combine_collapse/main.nf | 4 +-- .../combine_collapse/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/demux/main.nf | 4 +-- .../pixelator/demux/tests/main.nf.test.snap | 8 ++--- modules/local/pixelator/denoise/main.nf | 4 +-- .../pixelator/denoise/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/graph/main.nf | 4 +-- .../pixelator/graph/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/layout/main.nf | 4 +-- .../pixelator/layout/tests/main.nf.test.snap | 6 ++-- modules/local/pixelator/list_options/main.nf | 4 +-- .../local/pixelator/sample_calling/main.nf | 4 +-- .../sample_calling/tests/main.nf.test.snap | 4 +-- tests/proxiome_v1.nf.test.snap | 36 +++++++++---------- tests/proxiome_v2.nf.test.snap | 36 +++++++++---------- 22 files changed, 93 insertions(+), 83 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44f1cc99..d7904ab1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [[4.2.0dev](https://github.com/nf-core/pixelator/releases/tag/4.2.0)] - 2026-MM-DD +### Enhancements & fixes + +- Update pixelator container to 0.28.0 + +### Software dependencies + +| Dependency | Old version | New version | +| ----------- | ----------- | ----------- | +| `pixelator` | 0.27.2 | 0.28.0 | + ## [[4.1.1](https://github.com/nf-core/pixelator/releases/tag/4.1.1)] - 2026-05-29 ### Enhancements & fixes diff --git a/modules/local/pixelator/amplicon/main.nf b/modules/local/pixelator/amplicon/main.nf index a09a869b..991851d5 100644 --- a/modules/local/pixelator/amplicon/main.nf +++ b/modules/local/pixelator/amplicon/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_AMPLICON { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(reads, arity: '1..*') diff --git a/modules/local/pixelator/amplicon/tests/main.nf.test.snap b/modules/local/pixelator/amplicon/tests/main.nf.test.snap index 1b0ff6aa..fc57d4bb 100644 --- a/modules/local/pixelator/amplicon/tests/main.nf.test.snap +++ b/modules/local/pixelator/amplicon/tests/main.nf.test.snap @@ -60,7 +60,7 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.27.2" + "0.28.0" ] ], "amplicon": [ @@ -111,7 +111,7 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.27.2" + "0.28.0" ] ] } @@ -140,7 +140,7 @@ [ "PIXELATOR_AMPLICON", "pixelator", - "0.27.2" + "0.28.0" ] ] ], diff --git a/modules/local/pixelator/analysis/main.nf b/modules/local/pixelator/analysis/main.nf index 8377211f..96c727ef 100644 --- a/modules/local/pixelator/analysis/main.nf +++ b/modules/local/pixelator/analysis/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_ANALYSIS { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/analysis/tests/main.nf.test.snap b/modules/local/pixelator/analysis/tests/main.nf.test.snap index 97323df7..c0e533d1 100644 --- a/modules/local/pixelator/analysis/tests/main.nf.test.snap +++ b/modules/local/pixelator/analysis/tests/main.nf.test.snap @@ -17,7 +17,7 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -103,7 +103,7 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.27.2" + "0.28.0" ] ], "all_results": [ @@ -169,7 +169,7 @@ [ "PIXELATOR_ANALYSIS", "pixelator", - "0.27.2" + "0.28.0" ] ] } diff --git a/modules/local/pixelator/collapse/main.nf b/modules/local/pixelator/collapse/main.nf index 8f856602..f90ca932 100644 --- a/modules/local/pixelator/collapse/main.nf +++ b/modules/local/pixelator/collapse/main.nf @@ -7,8 +7,8 @@ process PIXELATOR_COLLAPSE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/collapse/tests/main.nf.test.snap b/modules/local/pixelator/collapse/tests/main.nf.test.snap index ada4ab07..f48263e8 100644 --- a/modules/local/pixelator/collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/collapse/tests/main.nf.test.snap @@ -17,7 +17,7 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -92,7 +92,7 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ], "collapsed": [ @@ -147,7 +147,7 @@ [ "PIXELATOR_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ] } diff --git a/modules/local/pixelator/combine_collapse/main.nf b/modules/local/pixelator/combine_collapse/main.nf index 71fbab63..c0c0bf63 100644 --- a/modules/local/pixelator/combine_collapse/main.nf +++ b/modules/local/pixelator/combine_collapse/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_COMBINE_COLLAPSE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(parquet_files, stageAs: "parquet/*"), path(json_report_files, stageAs: "reports/*") 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 add40a25..82e2bd96 100644 --- a/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap +++ b/modules/local/pixelator/combine_collapse/tests/main.nf.test.snap @@ -16,7 +16,7 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -87,7 +87,7 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ], "log": [ @@ -138,7 +138,7 @@ [ "PIXELATOR_COMBINE_COLLAPSE", "pixelator", - "0.27.2" + "0.28.0" ] ] } diff --git a/modules/local/pixelator/demux/main.nf b/modules/local/pixelator/demux/main.nf index ebbc9845..2a3fc150 100644 --- a/modules/local/pixelator/demux/main.nf +++ b/modules/local/pixelator/demux/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_DEMUX { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(reads), path(panel_file), val(panel), val(design) diff --git a/modules/local/pixelator/demux/tests/main.nf.test.snap b/modules/local/pixelator/demux/tests/main.nf.test.snap index 2f4c6e42..ed2d8618 100644 --- a/modules/local/pixelator/demux/tests/main.nf.test.snap +++ b/modules/local/pixelator/demux/tests/main.nf.test.snap @@ -20,7 +20,7 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -119,7 +119,7 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.27.2" + "0.28.0" ] ], "demuxed": [ @@ -195,7 +195,7 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.27.2" + "0.28.0" ] ] } @@ -241,7 +241,7 @@ [ "PIXELATOR_DEMUX", "pixelator", - "0.27.2" + "0.28.0" ] ] ], diff --git a/modules/local/pixelator/denoise/main.nf b/modules/local/pixelator/denoise/main.nf index a92ba82d..2648fdff 100644 --- a/modules/local/pixelator/denoise/main.nf +++ b/modules/local/pixelator/denoise/main.nf @@ -6,8 +6,8 @@ process PIXELATOR_DENOISE { // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/denoise/tests/main.nf.test.snap b/modules/local/pixelator/denoise/tests/main.nf.test.snap index 7347e3b6..89961abd 100644 --- a/modules/local/pixelator/denoise/tests/main.nf.test.snap +++ b/modules/local/pixelator/denoise/tests/main.nf.test.snap @@ -16,7 +16,7 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -102,7 +102,7 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.27.2" + "0.28.0" ] ], "all_results": [ @@ -168,7 +168,7 @@ [ "PIXELATOR_DENOISE", "pixelator", - "0.27.2" + "0.28.0" ] ] } diff --git a/modules/local/pixelator/graph/main.nf b/modules/local/pixelator/graph/main.nf index 0955e281..b45bd253 100644 --- a/modules/local/pixelator/graph/main.nf +++ b/modules/local/pixelator/graph/main.nf @@ -4,8 +4,8 @@ process PIXELATOR_GRAPH { label 'process_long' container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(edge_list), path(panel_file), val(panel) diff --git a/modules/local/pixelator/graph/tests/main.nf.test.snap b/modules/local/pixelator/graph/tests/main.nf.test.snap index 7209f331..ac7c1897 100644 --- a/modules/local/pixelator/graph/tests/main.nf.test.snap +++ b/modules/local/pixelator/graph/tests/main.nf.test.snap @@ -75,7 +75,7 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.27.2" + "0.28.0" ] ], "all_results": [ @@ -141,7 +141,7 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.27.2" + "0.28.0" ] ] } @@ -170,7 +170,7 @@ [ "PIXELATOR_GRAPH", "pixelator", - "0.27.2" + "0.28.0" ] ] ], diff --git a/modules/local/pixelator/layout/main.nf b/modules/local/pixelator/layout/main.nf index 9e3eb654..6a929361 100644 --- a/modules/local/pixelator/layout/main.nf +++ b/modules/local/pixelator/layout/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_LAYOUT { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'quay.io/pixelgen-technologies/pixelator:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/layout/tests/main.nf.test.snap b/modules/local/pixelator/layout/tests/main.nf.test.snap index 17cc8fa5..b291871e 100644 --- a/modules/local/pixelator/layout/tests/main.nf.test.snap +++ b/modules/local/pixelator/layout/tests/main.nf.test.snap @@ -17,7 +17,7 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.27.2" + "0.28.0" ] ] ], @@ -103,7 +103,7 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.27.2" + "0.28.0" ] ], "all_results": [ @@ -169,7 +169,7 @@ [ "PIXELATOR_LAYOUT", "pixelator", - "0.27.2" + "0.28.0" ] ] } diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf index 7ea881c0..ae5e0241 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:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" output: path "design_options.txt", emit: designs diff --git a/modules/local/pixelator/sample_calling/main.nf b/modules/local/pixelator/sample_calling/main.nf index 2f88cf9e..75c69ac4 100644 --- a/modules/local/pixelator/sample_calling/main.nf +++ b/modules/local/pixelator/sample_calling/main.nf @@ -5,8 +5,8 @@ process PIXELATOR_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:0.27.2' - : 'quay.io/pixelgen-technologies/pixelator:0.27.2'}" + ? 'quay.io/pixelgen-technologies/pixelator:0.28.0' + : 'quay.io/pixelgen-technologies/pixelator:0.28.0'}" input: tuple val(meta), path(data), path(samplesheet) 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 95d772b8..d5bca131 100644 --- a/modules/local/pixelator/sample_calling/tests/main.nf.test.snap +++ b/modules/local/pixelator/sample_calling/tests/main.nf.test.snap @@ -111,7 +111,7 @@ ] ], "6": [ - "versions.yml:md5,b92ce490993aa65332cf3e1fce6c4ff7" + "versions.yml:md5,caecdbbf67cdc742583ac0658769573d" ], "all_results": [ [ @@ -181,7 +181,7 @@ ] ], "versions": [ - "versions.yml:md5,b92ce490993aa65332cf3e1fce6c4ff7" + "versions.yml:md5,caecdbbf67cdc742583ac0658769573d" ] } ], diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index af2fdada..5a4a258f 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -117,31 +117,31 @@ "experiment-summary": "0.10.4" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "Workflow": { "nf-core/pixelator": "v4.2.0dev" @@ -165,31 +165,31 @@ "experiment-summary": "0.10.4" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "Workflow": { "nf-core/pixelator": "v4.2.0dev" diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index b36dd271..57f7df9f 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -154,31 +154,31 @@ "experiment-summary": "0.10.4" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "Workflow": { "nf-core/pixelator": "v4.2.0dev" @@ -202,31 +202,31 @@ "experiment-summary": "0.10.4" }, "PIXELATOR_AMPLICON": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_ANALYSIS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_COMBINE_COLLAPSE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DEMUX": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_DENOISE": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_GRAPH": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LAYOUT": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "PIXELATOR_LIST_OPTIONS": { - "pixelator": "0.27.2" + "pixelator": "0.28.0" }, "Workflow": { "nf-core/pixelator": "v4.2.0dev" From 8d53a4679b270a91c41cb9fdff3d4f0c63a5ea0c Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Thu, 4 Jun 2026 07:02:13 +0000 Subject: [PATCH 3/6] Clearer changelog --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d7904ab1..bf6b91f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,12 @@ 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). -## [[4.2.0dev](https://github.com/nf-core/pixelator/releases/tag/4.2.0)] - 2026-MM-DD +## [[4.1.2dev](https://github.com/nf-core/pixelator/releases/tag/4.1.1)] - 2026-MM-DD ### Enhancements & fixes -- Update pixelator container to 0.28.0 +- Update pixelator container to 0.28.0. This fixes a major performance regression + in the graph step, which caused very high memory usage. ### Software dependencies From 4b870d02f8b25f0a153139012ee831a47b28395c Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Thu, 4 Jun 2026 07:17:41 +0000 Subject: [PATCH 4/6] Set version target in nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index aab39cd9..1928c735 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.2.0dev' + version = '4.1.2dev' doi = '10.1101/2023.06.05.543770' } From d1271a0d2cde278007d35c5b3c39cd30922afd15 Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Thu, 4 Jun 2026 07:42:54 +0000 Subject: [PATCH 5/6] Update snapshots with new version targets --- tests/proxiome_v1.nf.test.snap | 4 ++-- tests/proxiome_v2.nf.test.snap | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index 5a4a258f..a8768c2c 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -144,7 +144,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.2.0dev" + "nf-core/pixelator": "v4.1.2dev" } } ], @@ -192,7 +192,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.2.0dev" + "nf-core/pixelator": "v4.1.2dev" } }, [ diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 57f7df9f..63d6da9f 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -181,7 +181,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.2.0dev" + "nf-core/pixelator": "v4.1.2dev" } } ], @@ -229,7 +229,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.2.0dev" + "nf-core/pixelator": "v4.1.2dev" } }, [ From de94c7a40d0165b76e5c6fa308a59f6c5b2a8580 Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Thu, 4 Jun 2026 08:16:23 +0000 Subject: [PATCH 6/6] Bump version to 4.1.2 --- .nf-core.yml | 2 +- CHANGELOG.md | 4 +-- nextflow.config | 2 +- ro-crate-metadata.json | 51 +++++++++++++++------------------- tests/proxiome_v1.nf.test.snap | 10 +++---- tests/proxiome_v2.nf.test.snap | 12 ++++---- 6 files changed, 38 insertions(+), 43 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index fe2ae4d6..bcfe64b6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -24,4 +24,4 @@ template: - fastqc - multiqc - igenomes - version: 4.2.0dev + version: 4.1.2 diff --git a/CHANGELOG.md b/CHANGELOG.md index bf6b91f6..b1bbe481 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,12 +3,12 @@ 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). -## [[4.1.2dev](https://github.com/nf-core/pixelator/releases/tag/4.1.1)] - 2026-MM-DD +## [[4.1.2](https://github.com/nf-core/pixelator/releases/tag/4.1.2)] - 2026-06-04 ### Enhancements & fixes - Update pixelator container to 0.28.0. This fixes a major performance regression - in the graph step, which caused very high memory usage. + in the graph step, which caused very high memory usage. By @johandahlberg [#221](https://github.com/nf-core/pixelator/pull/221) ### Software dependencies diff --git a/nextflow.config b/nextflow.config index 1928c735..937996fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.1.2dev' + version = '4.1.2' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 203e5807..05319757 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-05-29T13:57:42+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2026-06-04T07:56:31+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-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz\npool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,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/example_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": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#b08e9a66-f8b8-4587-9a7e-10048983d129" + "@id": "#047d5a72-e822-45cc-8115-f31953cae2be" } ], "name": "nf-core/pixelator" @@ -129,21 +129,19 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], - "author": [ + "creator": [ { "@id": "https://orcid.org/0009-0006-0086-2470" - } - ], - "contributor": [ + }, { - "@id": "https://orcid.org/0000-0001-6962-1460" + "@id": "#johan.dahlberg@pixelgen.tech" }, { - "@id": "https://orcid.org/0000-0001-5064-2093" + "@id": "https://orcid.org/0000-0003-2702-1103" } ], "dateCreated": "", - "dateModified": "2026-05-29T15:57:42Z", + "dateModified": "2026-06-04T07:56:31Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -161,6 +159,9 @@ "maintainer": [ { "@id": "https://orcid.org/0009-0006-0086-2470" + }, + { + "@id": "#johan.dahlberg@pixelgen.tech" } ], "name": [ @@ -174,10 +175,10 @@ }, "url": [ "https://github.com/nf-core/pixelator", - "https://nf-co.re/pixelator/dev/" + "https://nf-co.re/pixelator/4.1.2/" ], "version": [ - "4.2.0dev" + "4.1.2" ] }, { @@ -193,11 +194,11 @@ "version": "!>=25.10.4" }, { - "@id": "#b08e9a66-f8b8-4587-9a7e-10048983d129", + "@id": "#047d5a72-e822-45cc-8115-f31953cae2be", "@type": "TestSuite", "instance": [ { - "@id": "#1ea56774-5744-4332-bf43-225123fa4115" + "@id": "#b5a6d21f-6754-4699-931f-3a07a23b0818" } ], "mainEntity": { @@ -206,7 +207,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#1ea56774-5744-4332-bf43-225123fa4115", + "@id": "#b5a6d21f-6754-4699-931f-3a07a23b0818", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -342,26 +343,20 @@ { "@id": "https://orcid.org/0009-0006-0086-2470", "@type": "Person", - "affiliation": "Pixelgen Technologies AB", "email": "florian.detemmerman@pixelgen.com", - "name": "Florian De Temmerman", - "url": "https://github.com/fbdtemme" + "name": "Florian De Temmerman" }, { - "@id": "https://orcid.org/0000-0001-6962-1460", + "@id": "#johan.dahlberg@pixelgen.tech", "@type": "Person", - "affiliation": "Pixelgen Technologies AB", - "email": "johan.dahlberg@pixelgen.com", - "name": "Johan Dahlberg", - "url": "https://github.com/johandahlberg" + "email": "johan.dahlberg@pixelgen.tech", + "name": "Johan Dahlberg" }, { - "@id": "https://orcid.org/0000-0001-5064-2093", + "@id": "https://orcid.org/0000-0003-2702-1103", "@type": "Person", - "affiliation": "Pixelgen Technologies AB", - "email": "alvaro.martinez.barrio@pixelgen.com", - "name": "Alvaro Martinez Barrio", - "url": "https://github.com/ambarrio" + "email": "adrien.coulier@pixelgen.com", + "name": "Adrien Coulier" } ] } \ No newline at end of file diff --git a/tests/proxiome_v1.nf.test.snap b/tests/proxiome_v1.nf.test.snap index a8768c2c..90b8ccf0 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -144,11 +144,11 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2dev" + "nf-core/pixelator": "v4.1.2" } } ], - "timestamp": "2026-05-27T13:33:43.278926406", + "timestamp": "2026-06-04T08:06:20.429989163", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.5" @@ -192,7 +192,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2dev" + "nf-core/pixelator": "v4.1.2" } }, [ @@ -301,10 +301,10 @@ "sample_2.meta.json:md5,82fcbb6ae5e3156c70978973c862f5f3" ] ], - "timestamp": "2026-05-28T09:15:28.890062884", + "timestamp": "2026-06-04T08:05:33.528022276", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index 63d6da9f..225387e2 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -181,14 +181,14 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2dev" + "nf-core/pixelator": "v4.1.2" } } ], - "timestamp": "2026-05-28T09:17:00.841226981", + "timestamp": "2026-06-04T08:06:34.673086328", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } }, "Params: all": { @@ -229,7 +229,7 @@ "pixelator": "0.28.0" }, "Workflow": { - "nf-core/pixelator": "v4.1.2dev" + "nf-core/pixelator": "v4.1.2" } }, [ @@ -389,10 +389,10 @@ "sample4.meta.json:md5,f59cd8963a4760d34bd2b41e740242b7" ] ], - "timestamp": "2026-05-29T14:11:36.115348351", + "timestamp": "2026-06-04T08:05:44.413474873", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.5" } } } \ No newline at end of file