From edff12c8e21bd0534928f775a9b2925ccf3ab54a Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 9 Mar 2026 10:12:23 +0100 Subject: [PATCH 1/3] Remove if-statements from config --- conf/modules.config | 10 ---------- modules/local/experiment_summary/main.nf | 2 +- modules/local/pixelator/list_options/main.nf | 2 +- .../local/pixelator/single-cell-pna/amplicon/main.nf | 2 +- .../local/pixelator/single-cell-pna/analysis/main.nf | 2 +- .../local/pixelator/single-cell-pna/collapse/main.nf | 2 +- .../pixelator/single-cell-pna/combine_collapse/main.nf | 2 +- modules/local/pixelator/single-cell-pna/demux/main.nf | 2 +- .../local/pixelator/single-cell-pna/denoise/main.nf | 2 +- modules/local/pixelator/single-cell-pna/graph/main.nf | 2 +- modules/local/pixelator/single-cell-pna/layout/main.nf | 2 +- 11 files changed, 10 insertions(+), 20 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 0e80b750..29617ded 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -32,10 +32,6 @@ process { pattern: '*.log' ] ] - - if (params.pixelator_container) { - container = params.pixelator_container - } } withName: PIXELATOR_LIST_OPTIONS { @@ -45,10 +41,4 @@ process { withName: "CAT_FASTQ" { publishDir = [ enabled: false ] } - - withName: "EXPERIMENT_SUMMARY" { - if (params.experiment_summary_container) { - container = params.experiment_summary_container - } - } } diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf index 181ba20c..2967a5c1 100644 --- a/modules/local/experiment_summary/main.nf +++ b/modules/local/experiment_summary/main.nf @@ -2,7 +2,7 @@ process EXPERIMENT_SUMMARY { tag "${meta.id}" label "process_medium" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'quay.io/pixelgen-technologies/pixelatores:0.6.0' : 'quay.io/pixelgen-technologies/pixelatores:0.6.0'}" diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf index b3945806..dd24023f 100644 --- a/modules/local/pixelator/list_options/main.nf +++ b/modules/local/pixelator/list_options/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_LIST_OPTIONS { // TODO: Add conda back // conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/single-cell-pna/amplicon/main.nf index 0fb39f1a..ef0231c0 100644 --- a/modules/local/pixelator/single-cell-pna/amplicon/main.nf +++ b/modules/local/pixelator/single-cell-pna/amplicon/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_PNA_AMPLICON { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/analysis/main.nf b/modules/local/pixelator/single-cell-pna/analysis/main.nf index 31c536db..78cb0533 100644 --- a/modules/local/pixelator/single-cell-pna/analysis/main.nf +++ b/modules/local/pixelator/single-cell-pna/analysis/main.nf @@ -5,7 +5,7 @@ process PIXELATOR_PNA_ANALYSIS { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/collapse/main.nf b/modules/local/pixelator/single-cell-pna/collapse/main.nf index 7dec2a8a..4251de7c 100644 --- a/modules/local/pixelator/single-cell-pna/collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/collapse/main.nf @@ -6,7 +6,7 @@ process PIXELATOR_PNA_COLLAPSE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" 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 151d2fe9..3ecb4c19 100644 --- a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf +++ b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf @@ -5,7 +5,7 @@ process PIXELATOR_PNA_COMBINE_COLLAPSE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/demux/main.nf b/modules/local/pixelator/single-cell-pna/demux/main.nf index 9722e540..e2490760 100644 --- a/modules/local/pixelator/single-cell-pna/demux/main.nf +++ b/modules/local/pixelator/single-cell-pna/demux/main.nf @@ -5,7 +5,7 @@ process PIXELATOR_PNA_DEMUX { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/denoise/main.nf b/modules/local/pixelator/single-cell-pna/denoise/main.nf index cbb3d72a..02cb20ee 100644 --- a/modules/local/pixelator/single-cell-pna/denoise/main.nf +++ b/modules/local/pixelator/single-cell-pna/denoise/main.nf @@ -5,7 +5,7 @@ process PIXELATOR_PNA_DENOISE { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/graph/main.nf b/modules/local/pixelator/single-cell-pna/graph/main.nf index ad45a0eb..372a5cf4 100644 --- a/modules/local/pixelator/single-cell-pna/graph/main.nf +++ b/modules/local/pixelator/single-cell-pna/graph/main.nf @@ -3,7 +3,7 @@ process PIXELATOR_PNA_GRAPH { label 'process_high_memory' label 'process_long' - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" diff --git a/modules/local/pixelator/single-cell-pna/layout/main.nf b/modules/local/pixelator/single-cell-pna/layout/main.nf index d49794aa..0b85fbff 100644 --- a/modules/local/pixelator/single-cell-pna/layout/main.nf +++ b/modules/local/pixelator/single-cell-pna/layout/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_PNA_LAYOUT { // TODO: Add conda // conda "bioconda::pixelator=0.18.2" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${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'}" From f52b6075b02d2b18e7d8c22207cdefcb8199155c Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 9 Mar 2026 10:35:54 +0100 Subject: [PATCH 2/3] Bump version to 3.0.1 --- .nf-core.yml | 2 +- CHANGELOG.md | 5 +++++ nextflow.config | 2 +- ro-crate-metadata.json | 34 +++++++++++++++++----------------- tests/pna.nf.test.snap | 4 ++-- 5 files changed, 26 insertions(+), 21 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 76c9d634..d75c30b9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -23,4 +23,4 @@ template: - fastqc - multiqc - igenomes - version: 3.0.0 + version: 3.0.1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 66c046ee..bdc190b5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +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). +## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 + +### Enhancements & fixes +- Fix Issue #191 by @Aratz [#192](https://github.com/nf-core/pixelator/pull/183) + ## [[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..93d154a3 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 = '3.0.1' doi = '10.1101/2023.06.05.543770' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 22cf3cd8..50808df0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@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", + "datePublished": "2026-03-09T09:30:49+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": "#0937da83-39ee-4f26-ba19-81636de5941c" } ], "name": "nf-core/pixelator" @@ -131,17 +131,17 @@ ], "creator": [ { - "@id": "https://orcid.org/0009-0006-0086-2470" + "@id": "https://orcid.org/0000-0003-2702-1103" }, { - "@id": "https://orcid.org/0000-0003-2702-1103" + "@id": "https://orcid.org/0009-0006-0086-2470" }, { "@id": "#johan.dahlberg@pixelgen.tech" } ], "dateCreated": "", - "dateModified": "2026-02-23T08:30:51Z", + "dateModified": "2026-03-09T10:30:49Z", "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/3.0.1/" ], "version": [ - "3.0.0" + "3.0.1" ] }, { @@ -194,11 +194,11 @@ "version": "!>=25.04.0" }, { - "@id": "#9f9abf50-29d2-4cd8-be9c-9f2623f36243", + "@id": "#0937da83-39ee-4f26-ba19-81636de5941c", "@type": "TestSuite", "instance": [ { - "@id": "#941d74f8-288a-4b81-828b-bb4ed6d64d62" + "@id": "#a64c8985-335d-483b-9020-cc0dffd1d4a2" } ], "mainEntity": { @@ -207,7 +207,7 @@ "name": "Test suite for nf-core/pixelator" }, { - "@id": "#941d74f8-288a-4b81-828b-bb4ed6d64d62", + "@id": "#a64c8985-335d-483b-9020-cc0dffd1d4a2", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/pixelator", "resource": "repos/nf-core/pixelator/actions/workflows/nf-test.yml", @@ -340,18 +340,18 @@ "name": "nf-core", "url": "https://nf-co.re/" }, - { - "@id": "https://orcid.org/0009-0006-0086-2470", - "@type": "Person", - "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": "https://orcid.org/0009-0006-0086-2470", + "@type": "Person", + "email": "florian.detemmerman@pixelgen.com", + "name": "Florian De Temmerman" + }, { "@id": "#johan.dahlberg@pixelgen.tech", "@type": "Person", diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap index 193c79bc..50cfce97 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": "v3.0.1" } } ], @@ -154,7 +154,7 @@ "pixelator": "0.23.0" }, "Workflow": { - "nf-core/pixelator": "v3.0.0" + "nf-core/pixelator": "v3.0.1" } }, [ From 662aefab08b6842ca7867bd4f10b767e5f2cee53 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Mon, 9 Mar 2026 10:37:55 +0100 Subject: [PATCH 3/3] Apply prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bdc190b5..235298ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09 ### Enhancements & fixes + - Fix Issue #191 by @Aratz [#192](https://github.com/nf-core/pixelator/pull/183) ## [[3.0.0](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-02-23