diff --git a/.nf-core.yml b/.nf-core.yml index 47041fa7..243dcc37 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -14,4 +14,4 @@ template: name: nascent org: nf-core outdir: . - version: 2.3.0dev + version: 2.3.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 4269a9b3..ef22efa2 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). -## v2.3.0dev - [date] +## v2.3.0 - 2024-12-23 ### Added @@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#142](https://github.com/nf-core/nascent/pull/142) - Add STAR aligner - [#149](https://github.com/nf-core/nascent/pull/149) - Add Software citations to MultiQC - [#175](https://github.com/nf-core/nascent/pull/175) - Add HOMER uniqmap support +- [a3bc907](https://github.com/nf-core/nascent/commit/a3bc907e9afd9dd2a9572798fa16fbc781c3dcb0) - Update pipeline template to [nf-core/tools 2.13.1](https://github.com/nf-core/tools/releases/tag/2.13.1) +- [14fdbb8](https://github.com/nf-core/nascent/commit/14fdbb83fe944fc4d8d77e804f0332510d82fea4) - Update pipeline template to [nf-core/tools 3.0.0](https://github.com/nf-core/tools/releases/tag/3.0.0) +- [b4ac8c5](https://github.com/nf-core/nascent/commit/b4ac8c5) - Update pipeline template to [nf-core/tools 3.0.1](https://github.com/nf-core/tools/releases/tag/3.0.1) +- [a9ae47a](https://github.com/nf-core/nascent/commit/a9ae47a) - Update pipeline template to [nf-core/tools 3.0.1](https://github.com/nf-core/tools/releases/tag/3.0.2) +- [bfcd97c](https://github.com/nf-core/nascent/commit/bfcd97c) - Update pipeline template to [nf-core/tools 3.1.0](https://github.com/nf-core/tools/releases/tag/3.1.0) +- [7a4e356](https://github.com/nf-core/nascent/commit/7a4e356) - Update pipeline template to [nf-core/tools 3.1.1](https://github.com/nf-core/tools/releases/tag/3.1.1) ### Fixed diff --git a/README.md b/README.md index 10826c34..b1952d7b 100644 --- a/README.md +++ b/README.md @@ -94,7 +94,7 @@ For more details about the output files and reports, please refer to the nf-core/nascent was originally written by Ignacio Tripodi ([@ignaciot](https://github.com/ignaciot)) and Margaret Gruca ([@magruca](https://github.com/magruca)). -The pipeline was re-written in Nextflow DSL2 by Edmund Miller ([@Emiller88](https://github.com/emiller88)) and Sruthi Suresh ([@sruthipsuresh](https://github.com/sruthipsuresh)) from [The Functional Genomics Laboratory](https://taehoonkim.org/) at [The Univeristy of Texas at Dallas](https://www.utdallas.edu/) +The pipeline was re-written in Nextflow DSL2 by Edmund Miller ([@edmundmiller](https://github.com/edmundmiller)) and Sruthi Suresh ([@sruthipsuresh](https://github.com/sruthipsuresh)) from [The Functional Genomics Laboratory](https://taehoonkim.org/) at [The Univeristy of Texas at Dallas](https://www.utdallas.edu/) We thank the following people for their extensive assistance in the development of this pipeline: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 60f73877..1ed81747 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/nascent - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/nascent analysis pipeline. For information about how + to interpret these results, please see the documentation. report_section_order: fastqc: order: 4004 diff --git a/nextflow.config b/nextflow.config index 9a4c1790..651fcd84 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,29 +254,36 @@ manifest { name = 'nf-core/nascent' author = """Edmund Miller, Ignacio Tripodi, Margaret Gruca""" // 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: 'Edmund Miller', - affiliation: '', + affiliation: 'The Univeristy of Texas at Dallas', + email: 'nf-core@edmundmiller.dev', + github: 'edmundmiller', + contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: 'https://orcid.org/0000-0002-2398-0334' + ], + [ + name: 'Sruthi Suresh', + affiliation: 'The Univeristy of Texas at Dallas', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: 'sruthipsuresh', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], [ - name: ' Ignacio Tripodi', + name: 'Ignacio Tripodi', affiliation: '', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: 'ignaciot', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], [ - name: ' Margaret Gruca', + name: 'Margaret Gruca', affiliation: '', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: 'magruca', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '' ], ] @@ -285,7 +292,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '2.3.0dev' + version = '2.3.0' doi = '10.5281/zenodo.7245273' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 18932138..4851cb33 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T13:11:56+00:00", - "description": "

\n \n \n \"nf-core/nascent\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/nascent/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/nascent/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/nascent/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/nascent/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/nascent/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/nascent)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23nascent-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/nascent)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/nascent** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/nascent \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\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/nascent/usage) and the [parameter documentation](https://nf-co.re/nascent/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/nascent/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/nascent/output).\n\n## Credits\n\nnf-core/nascent was originally written by Edmund Miller, Ignacio Tripodi, Margaret Gruca.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#nascent` channel](https://nfcore.slack.com/channels/nascent) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\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", + "creativeWorkStatus": "Stable", + "datePublished": "2024-12-22T18:18:10+00:00", + "description": "

\n \n \n \"nf-core/nascent\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/nascent/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/nascent/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/nascent/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/nascent/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/nascent/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7245273-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7245273)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/nascent)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23nascent-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/nascent)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/nascent** is a bioinformatics best-practice analysis pipeline for nascent transcript (NT) and Transcriptional Start Site (TSS) assays.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/nascent/results).\n\n## Pipeline summary\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`fastp`](https://github.com/OpenGene/fastp))\n3. Alignment\n 1. [`bwa`](https://bio-bwa.sourceforge.net/)\n 2. [`bwamem2`](https://github.com/bwa-mem2/bwa-mem2)\n 3. [`DRAGMAP`](https://github.com/Illumina/DRAGMAP)\n4. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n5. UMI-based deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n6. Duplicate read marking ([`picard MarkDuplicates`](https://broadinstitute.github.io/picard/))\n7. Quality Control\n 1. [`RSeQC`](https://rseqc.sourceforge.net/index.html) - Various RNA-seq QC metrics\n 2. [`Preseq`](http://smithlabresearch.org/software/preseq/) - Estimation of library complexity\n 3. [`BBMap`](https://sourceforge.net/projects/bbmap/) - Analyzes the sequencing coverage\n8. Coverage Graphs\n 1. Create bedGraph coverage files ([`BEDTools`](https://github.com/arq5x/bedtools2/)\n 2. Create bigWig coverage files ([`deeptools`](https://deeptools.readthedocs.io/en/develop/))\n9. Transcript identification\n 1. [`HOMER`](http://homer.ucsd.edu/)\n 2. [`GroHMM`](https://bioconductor.org/packages/release/bioc/html/groHMM.html)\n 3. [`PINTS`](https://pints.yulab.org/)\n10. Quantification of Genes and Nascent Transcripts ([`featureCounts`](https://subread.sourceforge.net/featureCounts.html))\n11. Aggregate report describing results and QC from the whole pipeline ([`MultiQC`](http://multiqc.info/))\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\n\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/nascent \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\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/nascent/usage) and the [parameter documentation](https://nf-co.re/nascent/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/nascent/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/nascent/output).\n\n## Credits\n\nnf-core/nascent was originally written by Ignacio Tripodi ([@ignaciot](https://github.com/ignaciot)) and Margaret Gruca ([@magruca](https://github.com/magruca)).\n\nThe pipeline was re-written in Nextflow DSL2 by Edmund Miller ([@edmundmiller](https://github.com/edmundmiller)) and Sruthi Suresh ([@sruthipsuresh](https://github.com/sruthipsuresh)) from [The Functional Genomics Laboratory](https://taehoonkim.org/) at [The Univeristy of Texas at Dallas](https://www.utdallas.edu/)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@apeltzer](https://github.com/apeltzer)\n- [@ewels](https://github.com/ewels)\n- [@drpatelh](https://github.com/drpatelh)\n- [@pditommaso](https://github.com/pditommaso)\n- [@FriederikeHanssen](https://github.com/FriederikeHanssen)\n- [Tae Hoon Kim](https://github.com/taehoonkim-phd)\n- [@easterwoods](https://github.com/easterwoods)\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 `#nascent` channel](https://nfcore.slack.com/channels/nascent) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/nascent for your analysis, please cite it using the following doi: [10.5281/zenodo.7245273](https://doi.org/10.5281/zenodo.7245273)\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" @@ -31,6 +31,9 @@ { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -43,6 +46,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +105,7 @@ }, "mentions": [ { - "@id": "#1dfd475c-0e99-4ced-8d46-c7b1667f8062" + "@id": "#daaf6fca-5723-48f3-8e28-467003b1ba8b" } ], "name": "nf-core/nascent" @@ -129,10 +135,13 @@ "creator": [ { "@id": "https://orcid.org/0000-0002-6503-2180" + }, + { + "@id": "#git@edmundmiller.dev" } ], "dateCreated": "", - "dateModified": "2024-12-20T13:11:56Z", + "dateModified": "2024-12-22T12:18:10Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -147,6 +156,11 @@ "license": [ "MIT" ], + "maintainer": [ + { + "@id": "#git@edmundmiller.dev" + } + ], "name": [ "nf-core/nascent" ], @@ -158,10 +172,10 @@ }, "url": [ "https://github.com/nf-core/nascent", - "https://nf-co.re/nascent/dev/" + "https://nf-co.re/nascent/2.3.0/" ], "version": [ - "2.3.0dev" + "2.3.0" ] }, { @@ -177,11 +191,11 @@ "version": "!>=24.04.2" }, { - "@id": "#1dfd475c-0e99-4ced-8d46-c7b1667f8062", + "@id": "#daaf6fca-5723-48f3-8e28-467003b1ba8b", "@type": "TestSuite", "instance": [ { - "@id": "#3d1dd031-9b67-4d83-bdc1-e9f4277163af" + "@id": "#c8ba6d45-39ba-478f-a2d2-2ec121776d34" } ], "mainEntity": { @@ -190,7 +204,7 @@ "name": "Test suite for nf-core/nascent" }, { - "@id": "#3d1dd031-9b67-4d83-bdc1-e9f4277163af", + "@id": "#c8ba6d45-39ba-478f-a2d2-2ec121776d34", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/nascent", "resource": "repos/nf-core/nascent/actions/workflows/ci.yml", @@ -212,6 +226,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -232,6 +251,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -323,6 +347,12 @@ "@type": "Person", "email": "alex.peltzer@gmail.com", "name": "Alexander Peltzer" + }, + { + "@id": "https://orcid.org/0000-0002-6503-2180", + "@type": "Person", + "email": "nf-core@edmundmiller.dev", + "name": "Edmund Miller" } ] -} \ No newline at end of file +} diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap index 804a5398..632e62eb 100644 --- a/workflows/tests/aligner/bowtie2.nf.test.snap +++ b/workflows/tests/aligner/bowtie2.nf.test.snap @@ -87,7 +87,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap index 5bb2633d..7c3c7359 100644 --- a/workflows/tests/aligner/bwa.nf.test.snap +++ b/workflows/tests/aligner/bwa.nf.test.snap @@ -107,7 +107,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap index 257d9d93..bf3689a9 100644 --- a/workflows/tests/aligner/bwamem2.nf.test.snap +++ b/workflows/tests/aligner/bwamem2.nf.test.snap @@ -102,7 +102,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap index 815b8f9a..a4b9d13c 100644 --- a/workflows/tests/aligner/hisat2.nf.test.snap +++ b/workflows/tests/aligner/hisat2.nf.test.snap @@ -99,7 +99,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap index f19dd9c4..6b169b91 100644 --- a/workflows/tests/aligner/star.nf.test.snap +++ b/workflows/tests/aligner/star.nf.test.snap @@ -90,7 +90,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ @@ -465,7 +465,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } } ], diff --git a/workflows/tests/inputs/gff/main.nf.test.snap b/workflows/tests/inputs/gff/main.nf.test.snap index 1b41f1b6..1ebece28 100644 --- a/workflows/tests/inputs/gff/main.nf.test.snap +++ b/workflows/tests/inputs/gff/main.nf.test.snap @@ -87,7 +87,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap index f376150c..b18120b9 100644 --- a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap +++ b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap @@ -87,7 +87,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/inputs/only_gff/main.nf.test.snap b/workflows/tests/inputs/only_gff/main.nf.test.snap index c7fe6492..2e8f0e9f 100644 --- a/workflows/tests/inputs/only_gff/main.nf.test.snap +++ b/workflows/tests/inputs/only_gff/main.nf.test.snap @@ -90,7 +90,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/inputs/uniqmap/main.nf.test.snap b/workflows/tests/inputs/uniqmap/main.nf.test.snap index e194f434..c6833f9e 100644 --- a/workflows/tests/inputs/uniqmap/main.nf.test.snap +++ b/workflows/tests/inputs/uniqmap/main.nf.test.snap @@ -96,7 +96,7 @@ "7za": 16.02 }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } } ], diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap index c394efd9..d2d0c511 100644 --- a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap +++ b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap @@ -100,7 +100,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [ diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap index 877e3f4d..b147f03e 100644 --- a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap +++ b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap @@ -91,7 +91,7 @@ "subread": "2.0.1" }, "Workflow": { - "nf-core/nascent": "v2.3.0dev" + "nf-core/nascent": "v2.3.0" } }, [