From 2f5fa9c4b410fecbca0ce02b4da319b70a73715f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 28 May 2026 10:07:35 +0200 Subject: [PATCH 1/4] Update metromap --- docs/images/nf-core-pixelator-metromap.svg | 168 +++++++++++---------- 1 file changed, 85 insertions(+), 83 deletions(-) diff --git a/docs/images/nf-core-pixelator-metromap.svg b/docs/images/nf-core-pixelator-metromap.svg index 90af051b..1d1c8a2e 100644 --- a/docs/images/nf-core-pixelator-metromap.svg +++ b/docs/images/nf-core-pixelator-metromap.svg @@ -1,12 +1,12 @@ - + - + @@ -14,15 +14,16 @@ - - + + + - + - - - + + + @@ -33,7 +34,7 @@ - + @@ -42,7 +43,7 @@ - + @@ -64,25 +65,22 @@ - - - + + + + - - - - - - + + - - + + @@ -95,164 +93,168 @@ - - + + - - + + - + - + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - + + + + + + + + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - - + + - + - + - + - + - + - + - - + + From 6b8b86ebc47c4b3d2d0932498fa7b72aa2f45ff3 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 28 May 2026 10:13:16 +0200 Subject: [PATCH 2/4] Add missing icons --- nextflow_schema.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index dd6ba4cc..df50fdc2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -360,24 +360,28 @@ }, "pna_denoise_run_ace_denoising": { "type": "boolean", + "fa_icon": "fas fa-microscope", "description": "Remove nodes in the peripheral-like partition using adaptive core expansion (ACE).", "default": true }, "pna_denoise_ace_k": { "type": "integer", "description": "Neighborhood radius in graph steps for ACE denoising.", + "fa_icon": "far fa-circle", "default": 3, "minimum": 1, "maximum": 6 }, "pna_denoise_run_pls_denoising": { "type": "boolean", + "fa_icon": "fas fa-microscope", "description": "Run PLS-on-coreness denoising and retain the largest connected component after filtering.", "default": true }, "pna_denoise_pls_score_threshold": { "type": "number", "description": "All retained PLS score columns must exceed this value.", + "fa_icon": "fas fa-less-than-equal", "default": -3.0 } } From 0587d1293e3602a76a256cb9e88886f4c552c8e0 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 28 May 2026 10:17:22 +0200 Subject: [PATCH 3/4] Bump version to 4.1.0 --- .nf-core.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 18 +++++++++--------- tests/proxiome_v1.nf.test.snap | 4 ++-- tests/proxiome_v2.nf.test.snap | 4 ++-- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index a4f58321..7a1a3c52 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -24,4 +24,4 @@ template: - fastqc - multiqc - igenomes - version: 4.1.0dev + version: 4.1.0 diff --git a/nextflow.config b/nextflow.config index 59e0e315..b8fb0101 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.1.0dev' + version = '4.1.0' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 9cca5a06..733cbe6e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-05-25T06:35:05+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2026-05-28T08:13:39+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 --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": "#cbb02bf3-4ed9-4140-97b1-0307a5b2f6f7" + "@id": "#d36bde6c-c7d3-4c62-b1ff-1978ca784168" } ], "name": "nf-core/pixelator" @@ -143,7 +143,7 @@ } ], "dateCreated": "", - "dateModified": "2026-05-25T08:35:05Z", + "dateModified": "2026-05-28T10:13:39Z", "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/4.1.0/" ], "version": [ - "4.1.0dev" + "4.1.0" ] }, { @@ -193,11 +193,11 @@ "version": "!>=25.10.4" }, { - "@id": "#cbb02bf3-4ed9-4140-97b1-0307a5b2f6f7", + "@id": "#d36bde6c-c7d3-4c62-b1ff-1978ca784168", "@type": "TestSuite", "instance": [ { - "@id": "#4b4177e9-6e55-4ac1-8d33-5bc1b4db4128" + "@id": "#e2fe489f-4304-4725-9971-fe33067e7b77" } ], "mainEntity": { @@ -206,7 +206,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#4b4177e9-6e55-4ac1-8d33-5bc1b4db4128", + "@id": "#e2fe489f-4304-4725-9971-fe33067e7b77", "@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 a1e1d3ee..c28bec56 100644 --- a/tests/proxiome_v1.nf.test.snap +++ b/tests/proxiome_v1.nf.test.snap @@ -144,7 +144,7 @@ "pixelator": "0.27.1" }, "Workflow": { - "nf-core/pixelator": "v4.1.0dev" + "nf-core/pixelator": "v4.1.0" } } ], @@ -192,7 +192,7 @@ "pixelator": "0.27.1" }, "Workflow": { - "nf-core/pixelator": "v4.1.0dev" + "nf-core/pixelator": "v4.1.0" } }, [ diff --git a/tests/proxiome_v2.nf.test.snap b/tests/proxiome_v2.nf.test.snap index ab5d8542..4443677e 100644 --- a/tests/proxiome_v2.nf.test.snap +++ b/tests/proxiome_v2.nf.test.snap @@ -181,7 +181,7 @@ "pixelator": "0.27.1" }, "Workflow": { - "nf-core/pixelator": "v4.1.0dev" + "nf-core/pixelator": "v4.1.0" } } ], @@ -229,7 +229,7 @@ "pixelator": "0.27.1" }, "Workflow": { - "nf-core/pixelator": "v4.1.0dev" + "nf-core/pixelator": "v4.1.0" } }, [ From 0770f79c7bb342694ca03e4bdb3661297e887e2c Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 28 May 2026 10:20:54 +0200 Subject: [PATCH 4/4] Finalize changelog --- CHANGELOG.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b051127b..4d9cfd79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,17 +3,17 @@ 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). -## [[4.1.0dev](https://github.com/nf-core/pixelator/releases/tag/4.0.0)] - YYYY-MM-DD +## [[4.1.0](https://github.com/nf-core/pixelator/releases/tag/4.1.0)] - 2026-05-28 ### Enhancements & fixes -- Update pixelator container to 0.27.1 by @johandahlberg -- Denoise graph before sample calling step by @Aratz -- Add ACE and PLS denoising by @Aratz +- Update pixelator container to 0.27.1 by @johandahlberg [#212](https://github.com/nf-core/pixelator/pull/212) +- Denoise graph before sample calling step by @Aratz [#212](https://github.com/nf-core/pixelator/pull/212) +- Add ACE and PLS denoising by @Aratz [#212](https://github.com/nf-core/pixelator/pull/212) ### Changed -- K1 denoising is turned off by default by @Aratz +- K1 denoising is turned off by default by @Aratz [#212](https://github.com/nf-core/pixelator/pull/212) ### Software dependencies