diff --git a/CHANGELOG.md b/CHANGELOG.md index b2867ed97..fa8d95361 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -# 3.19.0dev - xxxx-xx-xx +# 3.19.0 - 2025-06-06 ### Credits @@ -37,6 +37,7 @@ Special thanks to the following for their contributions to the release: - [PR #1556](https://github.com/nf-core/rnaseq/pull/1556) - Update index docs to remove references to 'indexing only mode' - [PR #1558](https://github.com/nf-core/rnaseq/pull/1558) - Remove patches and bump modules for ARM compat - [PR #1560](https://github.com/nf-core/rnaseq/pull/1560) - General modules update, include updating subworkflows for stats fixes +- [PR #1563](https://github.com/nf-core/rnaseq/pull/1563) - Version bumps ahead of 3.19.0 release # 3.18.0 - 2024-12-19 diff --git a/nextflow.config b/nextflow.config index 0da93484b..1755be5bc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -346,29 +346,68 @@ manifest { name = 'nf-core/rnaseq' author = """Harshil Patel, Phil Ewels, Rickard Hammarén""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Harshil Patel', - affiliation: '', + affiliation: 'Seqera', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: '@drpatelh', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-2707-7940' + ], + [ + name: 'Jonathan Manning', + affiliation: 'Seqera', + email: '', + github: '@pinin4fjords', + contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-3483-8456' + ], + [ + name: 'Maxime Garcia', + affiliation: 'Seqera', + email: '', + github: '@maxulysse', + contribution: ['contributor', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], [ name: 'Phil Ewels', - affiliation: '', + affiliation: 'Seqera', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: '@ewels', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], + [ + name: 'Alexander Peltzer', + affiliation: 'Boehringer Ingelheim', + email: '', + github: '@apeltzer', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-6503-2180' + ], [ name: 'Rickard Hammarén', - affiliation: '', + affiliation: 'Scilifelab Data Centre', + email: '', + github: '@Hammarn', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0001-9017-591X' + ], + [ + name: 'Olga Botvinnik', + affiliation: 'Seanome', + email: '', + github: '@olgabot', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-4412-7970' + ], + [ + name: 'Adam Talbot', + affiliation: 'Seqera', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: '@adamrtalbot', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], ] @@ -377,7 +416,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '3.19.0dev' + version = '3.19.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index f5bac1122..6c4c523ea 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,16 +21,22 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2025-06-03T11:02:10+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2025-06-06T08:45:36+00:00", "description": "

\n \n \n \"nf-core/rnaseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)[![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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![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/rnaseq** is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.\n\n![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey_animated.svg)\n\n> In case the image above is not loading, please have a look at the [static version](docs/images/nf-core-rnaseq_metro_map_grey.png).\n\n1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))\n2. Auto-infer strandedness by subsampling and pseudoalignment ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))\n3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n5. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))\n6. Removal of genome contaminants ([`BBSplit`](http://seqanswers.com/forums/showthread.php?t=41288))\n7. Removal of ribosomal RNA ([`SortMeRNA`](https://github.com/biocore/sortmerna))\n8. Choice of multiple alignment and quantification routes:\n 1. [`STAR`](https://github.com/alexdobin/STAR) -> [`Salmon`](https://combine-lab.github.io/salmon/)\n 2. [`STAR`](https://github.com/alexdobin/STAR) -> [`RSEM`](https://github.com/deweylab/RSEM)\n 3. [`HiSAT2`](https://ccb.jhu.edu/software/hisat2/index.shtml) -> **NO QUANTIFICATION**\n9. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n10. UMI-based deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n11. Duplicate read marking ([`picard MarkDuplicates`](https://broadinstitute.github.io/picard/))\n12. Transcript assembly and quantification ([`StringTie`](https://ccb.jhu.edu/software/stringtie/))\n13. Create bigWig coverage files ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))\n14. Extensive quality control:\n 1. [`RSeQC`](http://rseqc.sourceforge.net/)\n 2. [`Qualimap`](http://qualimap.bioinfo.cipf.es/)\n 3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html)\n 4. [`Preseq`](http://smithlabresearch.org/software/preseq/)\n 5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)\n 6. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/) on unaligned sequences; _optional_\n15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)\n16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))\n\n> **Note**\n> The SRA download functionality has been removed from the pipeline (`>=3.2`) and ported to an independent workflow called [nf-core/fetchngs](https://nf-co.re/fetchngs). You can provide `--nf_core_pipeline rnaseq` when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline.\n\n> **Warning**\n> Quantification isn't performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.\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:\n\n**samplesheet.csv**:\n\n```csv\nsample,fastq_1,fastq_2,strandedness\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto\nCONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto\nCONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and will be automatically inferred if set to `auto`.\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\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/rnaseq \\\n --input \\\n --outdir \\\n --gtf \\\n --fasta \\\n -profile \n```\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/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/rnaseq/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/rnaseq/output).\n\nThis pipeline quantifies RNA-sequenced reads relative to genes/transcripts in the genome and normalizes the resulting data. It does not compare the samples statistically in order to assign significance in the form of FDR or P-values. For downstream analyses, the output files from this pipeline can be analysed directly in statistical environments like [R](https://www.r-project.org/), [Julia](https://julialang.org/) or via the [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance/) pipeline.\n\n## Online videos\n\nA short talk about the history, current status and functionality on offer in this pipeline was given by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) on [8th February 2022](https://nf-co.re/events/2022/bytesize-32-nf-core-rnaseq) as part of the nf-core/bytesize series.\n\nYou can find numerous talks on the [nf-core events page](https://nf-co.re/events) from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!\n\n## Credits\n\nThese scripts were originally written for use at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn)).\n\nThe pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/).\n\nThe pipeline workflow diagram was initially designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)) and James Fellows Yates ([@jfy133](https://github.com/jfy133)), further modifications where made by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and Maxime Garcia ([@maxulysse](https://github.com/maxulysse)).\n\nMany thanks to other who have helped out along the way too, including (but not limited to):\n\n- [Alex Peltzer](https://github.com/apeltzer)\n- [Colin Davenport](https://github.com/colindaven)\n- [Denis Moreno](https://github.com/Galithil)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Gregor Sturm](https://github.com/grst)\n- [Jacki Buros Novik](https://github.com/jburos)\n- [Lorena Pantano](https://github.com/lpantano)\n- [Matthias Zepper](https://github.com/MatthiasZepper)\n- [Maxime Garcia](https://github.com/maxulysse)\n- [Olga Botvinnik](https://github.com/olgabot)\n- [@orzechoj](https://github.com/orzechoj)\n- [Paolo Di Tommaso](https://github.com/pditommaso)\n- [Rob Syme](https://github.com/robsyme)\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 `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1400710](https://doi.org/10.5281/zenodo.1400710)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" }, + { + "@id": "docs/images/nf-core-rnaseq_metro_map_grey.png" + }, { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -43,6 +49,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +108,7 @@ }, "mentions": [ { - "@id": "#75f4967a-2681-475e-96a0-5ce5bc0521b7" + "@id": "#ae1587a7-b640-4951-835d-3d579ba3fbfd" } ], "name": "nf-core/rnaseq" @@ -128,12 +137,84 @@ ], "creator": [ { - "@id": "#phil.ewels@scilifelab.se" + "@id": "https://orcid.org/0000-0002-3859-3249" + }, + { + "@id": "#zhoupenggeni@gmail.com" + }, + { + "@id": "https://orcid.org/0009-0009-7515-5000" + }, + { + "@id": "https://orcid.org/0000-0002-5748-9594" + }, + { + "@id": "https://orcid.org/0000-0002-6503-2180" + }, + { + "@id": "https://orcid.org/0000-0002-8721-2350" + }, + { + "@id": "#jonathan.manning@seqera.io" + }, + { + "@id": "https://orcid.org/0000-0003-3220-0253" + }, + { + "@id": "#drpatelh@users.noreply.github.com" + }, + { + "@id": "#phil.ewels@seqera.io" + }, + { + "@id": "https://orcid.org/0000-0003-4412-7970" + }, + { + "@id": "#sven.fillinger@qbic.uni-tuebingen.de" + }, + { + "@id": "https://orcid.org/0000-0003-0603-7907" + }, + { + "@id": "#31933289+amayer21@users.noreply.github.com" + }, + { + "@id": "https://orcid.org/0000-0001-9584-7842" + }, + { + "@id": "https://orcid.org/0000-0003-3966-8481" + }, + { + "@id": "https://orcid.org/0000-0002-1968-2270" + }, + { + "@id": "#chuan.wang@scilifelab.se" + }, + { + "@id": "#zhenfeng.liu1@gmail.com" + }, + { + "@id": "https://orcid.org/0000-0002-8824-1946" + }, + { + "@id": "#omeally@gmail.com" + }, + { + "@id": "https://orcid.org/0000-0001-9017-591X" + }, + { + "@id": "https://orcid.org/0000-0002-2798-9870" + }, + { + "@id": "#42973691+d4straub@users.noreply.github.com" } ], "dateCreated": "", - "dateModified": "2025-06-03T11:02:10Z", + "dateModified": "2025-06-06T09:45:36Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "image": { + "@id": "docs/images/nf-core-rnaseq_metro_map_grey.png" + }, "keywords": [ "nf-core", "nextflow", @@ -145,7 +226,22 @@ ], "maintainer": [ { - "@id": "#phil.ewels@scilifelab.se" + "@id": "https://orcid.org/0000-0002-6503-2180" + }, + { + "@id": "#jonathan.manning@seqera.io" + }, + { + "@id": "#drpatelh@users.noreply.github.com" + }, + { + "@id": "#phil.ewels@seqera.io" + }, + { + "@id": "https://orcid.org/0000-0003-4412-7970" + }, + { + "@id": "https://orcid.org/0000-0001-9017-591X" } ], "name": [ @@ -159,10 +255,10 @@ }, "url": [ "https://github.com/nf-core/rnaseq", - "https://nf-co.re/rnaseq/dev/" + "https://nf-co.re/rnaseq/3.19.0/" ], "version": [ - "3.17.0dev" + "3.19.0" ] }, { @@ -178,11 +274,19 @@ "version": "!>=24.04.2" }, { - "@id": "#75f4967a-2681-475e-96a0-5ce5bc0521b7", + "@id": "docs/images/nf-core-rnaseq_metro_map_grey.png", + "@type": [ + "File", + "ImageObject" + ], + "name": "Workflow diagram" + }, + { + "@id": "#ae1587a7-b640-4951-835d-3d579ba3fbfd", "@type": "TestSuite", "instance": [ { - "@id": "#fa6744ce-944a-4de2-9c46-d4e1c31dba4b" + "@id": "#83e3a026-3fd3-4641-8c4c-6780c8c1d2fc" } ], "mainEntity": { @@ -191,7 +295,7 @@ "name": "Test suite for nf-core/rnaseq" }, { - "@id": "#fa6744ce-944a-4de2-9c46-d4e1c31dba4b", + "@id": "#83e3a026-3fd3-4641-8c4c-6780c8c1d2fc", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnaseq", "resource": "repos/nf-core/rnaseq/actions/workflows/nf-test.yml", @@ -213,6 +317,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -233,6 +342,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -320,10 +434,148 @@ "url": "https://nf-co.re/" }, { - "@id": "#phil.ewels@scilifelab.se", + "@id": "https://orcid.org/0000-0002-3859-3249", + "@type": "Person", + "email": "lorena.pantano@gmail.com", + "name": "Lorena Pantano" + }, + { + "@id": "#zhoupenggeni@gmail.com", + "@type": "Person", + "email": "zhoupenggeni@gmail.com", + "name": "Peng Zhou" + }, + { + "@id": "https://orcid.org/0009-0009-7515-5000", + "@type": "Person", + "email": "sofia.haglund@scilifelab.se", + "name": "Sofia Haglund" + }, + { + "@id": "https://orcid.org/0000-0002-5748-9594", + "@type": "Person", + "email": "pranathi93.vemuri@gmail.com", + "name": "Pranathi Vemuri" + }, + { + "@id": "https://orcid.org/0000-0002-6503-2180", + "@type": "Person", + "email": "apeltzer@users.noreply.github.com", + "name": "Alexander Peltzer" + }, + { + "@id": "https://orcid.org/0000-0002-8721-2350", + "@type": "Person", + "email": "rob.syme@gmail.com", + "name": "Robert Syme" + }, + { + "@id": "#jonathan.manning@seqera.io", + "@type": "Person", + "email": "jonathan.manning@seqera.io", + "name": "Jonathan Manning" + }, + { + "@id": "https://orcid.org/0000-0003-3220-0253", + "@type": "Person", + "email": "paolo.ditommaso@gmail.com", + "name": "Paolo Di Tommaso" + }, + { + "@id": "#drpatelh@users.noreply.github.com", + "@type": "Person", + "email": "drpatelh@users.noreply.github.com", + "name": "Harshil Patel" + }, + { + "@id": "#phil.ewels@seqera.io", "@type": "Person", - "email": "phil.ewels@scilifelab.se", + "email": "phil.ewels@seqera.io", "name": "Phil Ewels" + }, + { + "@id": "https://orcid.org/0000-0003-4412-7970", + "@type": "Person", + "email": "olga.botvinnik@gmail.com", + "name": "Olga Botvinnik" + }, + { + "@id": "#sven.fillinger@qbic.uni-tuebingen.de", + "@type": "Person", + "email": "sven.fillinger@qbic.uni-tuebingen.de", + "name": "Sven F" + }, + { + "@id": "https://orcid.org/0000-0003-0603-7907", + "@type": "Person", + "email": "sabrina.krakau@qbic.uni-tuebingen.de", + "name": "Sabrina Krakau" + }, + { + "@id": "#31933289+amayer21@users.noreply.github.com", + "@type": "Person", + "email": "31933289+amayer21@users.noreply.github.com", + "name": "Alice Mayer" + }, + { + "@id": "https://orcid.org/0000-0001-9584-7842", + "@type": "Person", + "email": "mail@gregor-sturm.de", + "name": "Gregor Sturm" + }, + { + "@id": "https://orcid.org/0000-0003-3966-8481", + "@type": "Person", + "email": "pcantalupo@gmail.com", + "name": "Paul Cantalupo" + }, + { + "@id": "https://orcid.org/0000-0002-1968-2270", + "@type": "Person", + "email": "anandasanil@gmail.com", + "name": "Anandashankar Anil" + }, + { + "@id": "#chuan.wang@scilifelab.se", + "@type": "Person", + "email": "chuan.wang@scilifelab.se", + "name": "Chuan Wang" + }, + { + "@id": "#zhenfeng.liu1@gmail.com", + "@type": "Person", + "email": "zhenfeng.liu1@gmail.com", + "name": "Zhenfeng Liu" + }, + { + "@id": "https://orcid.org/0000-0002-8824-1946", + "@type": "Person", + "email": "gisela.gabernet@gmail.com", + "name": "Gisela Gabernet Garriga" + }, + { + "@id": "#omeally@gmail.com", + "@type": "Person", + "email": "omeally@gmail.com", + "name": "Denis OMeally" + }, + { + "@id": "https://orcid.org/0000-0001-9017-591X", + "@type": "Person", + "email": "rickard.hammaren@scilifelab.se", + "name": "Rickard Hammar\u00e9n" + }, + { + "@id": "https://orcid.org/0000-0002-2798-9870", + "@type": "Person", + "email": "silvia.morini01@gmail.com", + "name": "Silvia Morini" + }, + { + "@id": "#42973691+d4straub@users.noreply.github.com", + "@type": "Person", + "email": "42973691+d4straub@users.noreply.github.com", + "name": "Daniel Straub" } ] } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 7eaad0b40..82632a9ed 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -47,7 +47,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -245,7 +245,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 376a2507c..b5ec7924a 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -47,7 +47,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -239,7 +239,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 807d286cf..592344ef2 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -48,7 +48,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -242,7 +242,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index fa5c13f87..43ed24891 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -63,7 +63,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -320,7 +320,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 25dc5f3ba..13f7db506 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -141,7 +141,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1241,7 +1241,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap index 7573257c2..7653d7b9d 100644 --- a/tests/nofasta.nf.test.snap +++ b/tests/nofasta.nf.test.snap @@ -52,7 +52,7 @@ "bioconductor-tximeta": "1.20.1" }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index c1cc9d79c..10e04c209 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -147,7 +147,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1453,7 +1453,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index d42660007..424dd917b 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -57,7 +57,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -393,7 +393,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index a91e41e83..0686bdc8b 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -187,7 +187,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 09f09a895..8411faa73 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -136,7 +136,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index e01378a1a..da65d6b61 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -141,7 +141,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1335,7 +1335,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index 7c81391ba..9fd7a2f31 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -144,7 +144,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1637,7 +1637,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ @@ -2782,7 +2782,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.19.0dev" + "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 9a98b1705..a60c89347 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how - to interpret these results, please see the documentation. report_section_order: # Important checks and failures