diff --git a/.nf-core.yml b/.nf-core.yml index b2daedda3..463d73fef 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -13,7 +13,7 @@ lint: nf_core_version: 3.3.1 repository_type: pipeline template: - author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n" + author: "Harshil Patel, Phil Ewels, Rickard Hammarén" description: RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control. force: false @@ -21,4 +21,4 @@ template: name: rnaseq org: nf-core outdir: . - version: 3.19.0 + version: 3.20.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 580c077d3..0e3040977 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,20 @@ 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). -# 3.19.0 - 2025-06-06 +## 3.20.0dev + +### Credits + +Special thanks to the following for their contributions to the release: + +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Maxime Garcia](https://github.com/maxulysse) + +### Enhancements & fixes + +- [PR #1568](https://github.com/nf-core/rnaseq/pull/1568) - Bump version after release 3.19.0 + +## [[3.19.0](https://github.com/nf-core/rnaseq/releases/tag/3.19.0)] - 2025-06-10 ### Credits @@ -15,6 +28,7 @@ Special thanks to the following for their contributions to the release: - [Ben Sherman](https://github.com/bentsherman) - [Dave Carlson](https://github.com/davidecarlson) - [Gabriel Lichtenstein](https://github.com/glichtenstein) +- [Jonathan Manning](https://github.com/pinin4fjords) - [Lorenzo Fontana](https://github.com/fntlnz) - [Matthias Hörtenhuber](https://github.com/mashehu) - [Milos Micik](https://github.com/milos7250) @@ -41,7 +55,7 @@ Special thanks to the following for their contributions to the release: - [PR #1565](https://github.com/nf-core/rnaseq/pull/1565) - Improve reproducibility with Conda - [PR #1567](https://github.com/nf-core/rnaseq/pull/1567) - Prerelease 3.19.0 fixes -# 3.18.0 - 2024-12-19 +## [[3.18.0](https://github.com/nf-core/rnaseq/releases/tag/3.18.0)] - 2024-12-19 ### Credits diff --git a/nextflow.config b/nextflow.config index 1755be5bc..c0a6c908e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -416,7 +416,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '3.19.0' + version = '3.20.0dev' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/nf-test.config b/nf-test.config index fe148de9f..59c90c5dd 100644 --- a/nf-test.config +++ b/nf-test.config @@ -20,6 +20,6 @@ config { // load the necessary plugins plugins { load "nft-bam@0.4.0" - load "nft-utils@0.0.3" + load "nft-utils@0.0.4" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 6c4c523ea..e2eeca986 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2025-06-06T08:45:36+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2025-06-10T11:59:03+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": [ { @@ -108,7 +108,7 @@ }, "mentions": [ { - "@id": "#ae1587a7-b640-4951-835d-3d579ba3fbfd" + "@id": "#e0772cda-30d9-43ea-a716-1d8bebbf11ac" } ], "name": "nf-core/rnaseq" @@ -137,80 +137,80 @@ ], "creator": [ { - "@id": "https://orcid.org/0000-0002-3859-3249" - }, - { - "@id": "#zhoupenggeni@gmail.com" + "@id": "https://orcid.org/0000-0002-8721-2350" }, { "@id": "https://orcid.org/0009-0009-7515-5000" }, { - "@id": "https://orcid.org/0000-0002-5748-9594" + "@id": "https://orcid.org/0000-0003-0603-7907" }, { - "@id": "https://orcid.org/0000-0002-6503-2180" + "@id": "https://orcid.org/0000-0002-2798-9870" }, { - "@id": "https://orcid.org/0000-0002-8721-2350" + "@id": "https://orcid.org/0000-0003-3966-8481" }, { - "@id": "#jonathan.manning@seqera.io" + "@id": "https://orcid.org/0000-0003-4412-7970" }, { - "@id": "https://orcid.org/0000-0003-3220-0253" + "@id": "#sven.fillinger@qbic.uni-tuebingen.de" }, { "@id": "#drpatelh@users.noreply.github.com" }, { - "@id": "#phil.ewels@seqera.io" + "@id": "#chuan.wang@scilifelab.se" }, { - "@id": "https://orcid.org/0000-0003-4412-7970" + "@id": "https://orcid.org/0000-0002-3859-3249" }, { - "@id": "#sven.fillinger@qbic.uni-tuebingen.de" + "@id": "https://orcid.org/0000-0002-6503-2180" }, { - "@id": "https://orcid.org/0000-0003-0603-7907" + "@id": "#phil.ewels@seqera.io" }, { - "@id": "#31933289+amayer21@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-5748-9594" }, { - "@id": "https://orcid.org/0000-0001-9584-7842" + "@id": "https://orcid.org/0000-0002-1968-2270" }, { - "@id": "https://orcid.org/0000-0003-3966-8481" + "@id": "https://orcid.org/0000-0001-9017-591X" }, { - "@id": "https://orcid.org/0000-0002-1968-2270" + "@id": "#zhoupenggeni@gmail.com" }, { - "@id": "#chuan.wang@scilifelab.se" + "@id": "#jonathan.manning@seqera.io" }, { "@id": "#zhenfeng.liu1@gmail.com" }, { - "@id": "https://orcid.org/0000-0002-8824-1946" + "@id": "https://orcid.org/0000-0003-3220-0253" }, { - "@id": "#omeally@gmail.com" + "@id": "#31933289+amayer21@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0001-9017-591X" + "@id": "https://orcid.org/0000-0002-8824-1946" }, { - "@id": "https://orcid.org/0000-0002-2798-9870" + "@id": "https://orcid.org/0000-0001-9584-7842" + }, + { + "@id": "#omeally@gmail.com" }, { "@id": "#42973691+d4straub@users.noreply.github.com" } ], "dateCreated": "", - "dateModified": "2025-06-06T09:45:36Z", + "dateModified": "2025-06-10T13:59:03Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "image": { "@id": "docs/images/nf-core-rnaseq_metro_map_grey.png" @@ -226,22 +226,22 @@ ], "maintainer": [ { - "@id": "https://orcid.org/0000-0002-6503-2180" + "@id": "https://orcid.org/0000-0003-4412-7970" }, { - "@id": "#jonathan.manning@seqera.io" + "@id": "#drpatelh@users.noreply.github.com" }, { - "@id": "#drpatelh@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-6503-2180" }, { "@id": "#phil.ewels@seqera.io" }, { - "@id": "https://orcid.org/0000-0003-4412-7970" + "@id": "https://orcid.org/0000-0001-9017-591X" }, { - "@id": "https://orcid.org/0000-0001-9017-591X" + "@id": "#jonathan.manning@seqera.io" } ], "name": [ @@ -255,10 +255,10 @@ }, "url": [ "https://github.com/nf-core/rnaseq", - "https://nf-co.re/rnaseq/3.19.0/" + "https://nf-co.re/rnaseq/dev/" ], "version": [ - "3.19.0" + "3.20.0dev" ] }, { @@ -282,11 +282,11 @@ "name": "Workflow diagram" }, { - "@id": "#ae1587a7-b640-4951-835d-3d579ba3fbfd", + "@id": "#e0772cda-30d9-43ea-a716-1d8bebbf11ac", "@type": "TestSuite", "instance": [ { - "@id": "#83e3a026-3fd3-4641-8c4c-6780c8c1d2fc" + "@id": "#94149752-60aa-413b-ab38-be09b1fc43a2" } ], "mainEntity": { @@ -295,7 +295,7 @@ "name": "Test suite for nf-core/rnaseq" }, { - "@id": "#83e3a026-3fd3-4641-8c4c-6780c8c1d2fc", + "@id": "#94149752-60aa-413b-ab38-be09b1fc43a2", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnaseq", "resource": "repos/nf-core/rnaseq/actions/workflows/nf-test.yml", @@ -434,16 +434,10 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0002-3859-3249", - "@type": "Person", - "email": "lorena.pantano@gmail.com", - "name": "Lorena Pantano" - }, - { - "@id": "#zhoupenggeni@gmail.com", + "@id": "https://orcid.org/0000-0002-8721-2350", "@type": "Person", - "email": "zhoupenggeni@gmail.com", - "name": "Peng Zhou" + "email": "rob.syme@gmail.com", + "name": "Robert Syme" }, { "@id": "https://orcid.org/0009-0009-7515-5000", @@ -452,34 +446,34 @@ "name": "Sofia Haglund" }, { - "@id": "https://orcid.org/0000-0002-5748-9594", + "@id": "https://orcid.org/0000-0003-0603-7907", "@type": "Person", - "email": "pranathi93.vemuri@gmail.com", - "name": "Pranathi Vemuri" + "email": "sabrina.krakau@qbic.uni-tuebingen.de", + "name": "Sabrina Krakau" }, { - "@id": "https://orcid.org/0000-0002-6503-2180", + "@id": "https://orcid.org/0000-0002-2798-9870", "@type": "Person", - "email": "apeltzer@users.noreply.github.com", - "name": "Alexander Peltzer" + "email": "silvia.morini01@gmail.com", + "name": "Silvia Morini" }, { - "@id": "https://orcid.org/0000-0002-8721-2350", + "@id": "https://orcid.org/0000-0003-3966-8481", "@type": "Person", - "email": "rob.syme@gmail.com", - "name": "Robert Syme" + "email": "pcantalupo@gmail.com", + "name": "Paul Cantalupo" }, { - "@id": "#jonathan.manning@seqera.io", + "@id": "https://orcid.org/0000-0003-4412-7970", "@type": "Person", - "email": "jonathan.manning@seqera.io", - "name": "Jonathan Manning" + "email": "olga.botvinnik@gmail.com", + "name": "Olga Botvinnik" }, { - "@id": "https://orcid.org/0000-0003-3220-0253", + "@id": "#sven.fillinger@qbic.uni-tuebingen.de", "@type": "Person", - "email": "paolo.ditommaso@gmail.com", - "name": "Paolo Di Tommaso" + "email": "sven.fillinger@qbic.uni-tuebingen.de", + "name": "Sven F" }, { "@id": "#drpatelh@users.noreply.github.com", @@ -488,58 +482,58 @@ "name": "Harshil Patel" }, { - "@id": "#phil.ewels@seqera.io", + "@id": "#chuan.wang@scilifelab.se", "@type": "Person", - "email": "phil.ewels@seqera.io", - "name": "Phil Ewels" + "email": "chuan.wang@scilifelab.se", + "name": "Chuan Wang" }, { - "@id": "https://orcid.org/0000-0003-4412-7970", + "@id": "https://orcid.org/0000-0002-3859-3249", "@type": "Person", - "email": "olga.botvinnik@gmail.com", - "name": "Olga Botvinnik" + "email": "lorena.pantano@gmail.com", + "name": "Lorena Pantano" }, { - "@id": "#sven.fillinger@qbic.uni-tuebingen.de", + "@id": "https://orcid.org/0000-0002-6503-2180", "@type": "Person", - "email": "sven.fillinger@qbic.uni-tuebingen.de", - "name": "Sven F" + "email": "apeltzer@users.noreply.github.com", + "name": "Alexander Peltzer" }, { - "@id": "https://orcid.org/0000-0003-0603-7907", + "@id": "#phil.ewels@seqera.io", "@type": "Person", - "email": "sabrina.krakau@qbic.uni-tuebingen.de", - "name": "Sabrina Krakau" + "email": "phil.ewels@seqera.io", + "name": "Phil Ewels" }, { - "@id": "#31933289+amayer21@users.noreply.github.com", + "@id": "https://orcid.org/0000-0002-5748-9594", "@type": "Person", - "email": "31933289+amayer21@users.noreply.github.com", - "name": "Alice Mayer" + "email": "pranathi93.vemuri@gmail.com", + "name": "Pranathi Vemuri" }, { - "@id": "https://orcid.org/0000-0001-9584-7842", + "@id": "https://orcid.org/0000-0002-1968-2270", "@type": "Person", - "email": "mail@gregor-sturm.de", - "name": "Gregor Sturm" + "email": "anandasanil@gmail.com", + "name": "Anandashankar Anil" }, { - "@id": "https://orcid.org/0000-0003-3966-8481", + "@id": "https://orcid.org/0000-0001-9017-591X", "@type": "Person", - "email": "pcantalupo@gmail.com", - "name": "Paul Cantalupo" + "email": "rickard.hammaren@scilifelab.se", + "name": "Rickard Hammar\u00e9n" }, { - "@id": "https://orcid.org/0000-0002-1968-2270", + "@id": "#zhoupenggeni@gmail.com", "@type": "Person", - "email": "anandasanil@gmail.com", - "name": "Anandashankar Anil" + "email": "zhoupenggeni@gmail.com", + "name": "Peng Zhou" }, { - "@id": "#chuan.wang@scilifelab.se", + "@id": "#jonathan.manning@seqera.io", "@type": "Person", - "email": "chuan.wang@scilifelab.se", - "name": "Chuan Wang" + "email": "jonathan.manning@seqera.io", + "name": "Jonathan Manning" }, { "@id": "#zhenfeng.liu1@gmail.com", @@ -548,28 +542,34 @@ "name": "Zhenfeng Liu" }, { - "@id": "https://orcid.org/0000-0002-8824-1946", + "@id": "https://orcid.org/0000-0003-3220-0253", "@type": "Person", - "email": "gisela.gabernet@gmail.com", - "name": "Gisela Gabernet Garriga" + "email": "paolo.ditommaso@gmail.com", + "name": "Paolo Di Tommaso" }, { - "@id": "#omeally@gmail.com", + "@id": "#31933289+amayer21@users.noreply.github.com", "@type": "Person", - "email": "omeally@gmail.com", - "name": "Denis OMeally" + "email": "31933289+amayer21@users.noreply.github.com", + "name": "Alice Mayer" }, { - "@id": "https://orcid.org/0000-0001-9017-591X", + "@id": "https://orcid.org/0000-0002-8824-1946", "@type": "Person", - "email": "rickard.hammaren@scilifelab.se", - "name": "Rickard Hammar\u00e9n" + "email": "gisela.gabernet@gmail.com", + "name": "Gisela Gabernet Garriga" }, { - "@id": "https://orcid.org/0000-0002-2798-9870", + "@id": "https://orcid.org/0000-0001-9584-7842", "@type": "Person", - "email": "silvia.morini01@gmail.com", - "name": "Silvia Morini" + "email": "mail@gregor-sturm.de", + "name": "Gregor Sturm" + }, + { + "@id": "#omeally@gmail.com", + "@type": "Person", + "email": "omeally@gmail.com", + "name": "Denis OMeally" }, { "@id": "#42973691+d4straub@users.noreply.github.com", diff --git a/tests/default.nf.test b/tests/default.nf.test index 1ae3c8006..a1dd49e13 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -22,8 +22,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -53,8 +53,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3a80e40c1..68290e58d 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -34,20 +34,17 @@ "gunzip": 1.13 }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -126,12 +123,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -212,14 +209,14 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" @@ -228,9 +225,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -243,9 +240,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index b4c711478..6827887a4 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 1eccfe27e..592a64b64 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -34,20 +34,17 @@ "gunzip": 1.13 }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -126,12 +123,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -209,22 +206,22 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -237,9 +234,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 5ae168692..a0f0454b8 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 61c905b59..925652fdb 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -37,18 +37,15 @@ "hisat2": "2.2.1" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -127,8 +124,8 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -222,9 +219,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -240,9 +237,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 18b7b7b4e..a67b2d314 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -25,8 +25,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -59,8 +59,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 43ed24891..1aea9ebe9 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -52,18 +52,15 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -312,15 +309,12 @@ "kallisto": "0.51.1" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 33b5a17af..b0fa950e7 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 4868c9ac9..0da29ae94 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -22,12 +22,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -108,14 +108,14 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" @@ -124,9 +124,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -139,9 +139,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1226,20 +1223,17 @@ "gunzip": 1.13 }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/nofasta.nf.test b/tests/nofasta.nf.test index 27cadd6af..f8fcb5880 100644 --- a/tests/nofasta.nf.test +++ b/tests/nofasta.nf.test @@ -27,8 +27,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap index 5808d1a2d..f7cc0d557 100644 --- a/tests/nofasta.nf.test.snap +++ b/tests/nofasta.nf.test.snap @@ -10,8 +10,8 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "FASTQC": { "fastqc": "0.12.1" @@ -44,15 +44,12 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 590a21faa..8128a85a5 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 8621eb648..46ed3b163 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -22,12 +22,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -114,14 +114,14 @@ "sortmerna": "4.3.7" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" @@ -130,9 +130,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -145,9 +145,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1438,20 +1435,17 @@ "sortmerna": "4.3.7" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 410b3f744..3bf6168e5 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -25,8 +25,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -59,8 +59,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 424dd917b..989b8331e 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -46,18 +46,15 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -385,15 +382,12 @@ "gunzip": 1.13 }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index cbbf53681..0c6967705 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 0686bdc8b..3d2c362b5 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -31,20 +31,17 @@ "gunzip": 1.13 }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -157,22 +154,22 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -185,9 +182,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 5e5ea702e..43d07ed7b 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index b1f4eb4b3..2f1688187 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -22,12 +22,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -108,14 +108,14 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" @@ -134,9 +134,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 33d05f50a..dcebcb69a 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,8 +55,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 6ff1e2fca..d2f04cdf1 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -22,12 +22,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_RSEM": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -121,9 +121,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -139,9 +139,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1322,18 +1319,15 @@ "gunzip": 1.13 }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UNTAR_RSEM_INDEX": { "untar": 1.34 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ diff --git a/tests/umi.nf.test b/tests/umi.nf.test index 6a417cb14..9bc9506e4 100644 --- a/tests/umi.nf.test +++ b/tests/umi.nf.test @@ -30,8 +30,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -65,8 +65,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -100,8 +100,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index f57dddadd..e2235b926 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -19,12 +19,12 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DESEQ2_QC_STAR_SALMON": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -102,14 +102,14 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" @@ -118,9 +118,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -142,9 +142,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -1517,8 +1514,8 @@ "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { - "r-base": "4.0.3", - "bioconductor-deseq2": "1.28.0" + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" @@ -1609,9 +1606,9 @@ "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1633,9 +1630,6 @@ }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "nf-core/rnaseq": "v3.19.0" } }, [ @@ -2763,23 +2757,20 @@ "gunzip": 1.13 }, "STAR_GENOMEGENERATE": { - "star": "2.7.11b", + "gawk": "5.1.0", "samtools": 1.21, - "gawk": "5.1.0" + "star": "2.7.11b" }, "TRIMGALORE": { - "trimgalore": "0.6.10", "cutadapt": 4.9, - "pigz": 2.8 + "pigz": 2.8, + "trimgalore": "0.6.10" }, "UMITOOLS_EXTRACT": { "umitools": "1.1.5" }, "UNTAR_SALMON_INDEX": { "untar": 1.34 - }, - "Workflow": { - "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 a60c89347..9a98b1705 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