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Merged
pinin4fjords merged 3 commits into from
Jun 6, 2025
Merged

Version bumps ahead of 3.19.0 release #1563

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a36b70a
Bump versions
pinin4fjords Jun 6, 2025
40765eb
update changelog
pinin4fjords Jun 6, 2025
5e540d8
Prettier multiqc config
pinin4fjords Jun 6, 2025
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

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61 changes: 50 additions & 11 deletions nextflow.config
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Expand Up @@ -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: ''
],
]
Expand All @@ -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'
}

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278 changes: 265 additions & 13 deletions ro-crate-metadata.json
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4 changes: 2 additions & 2 deletions tests/default.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -245,7 +245,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/featurecounts_group_type.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -239,7 +239,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/hisat2.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -242,7 +242,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/kallisto.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -320,7 +320,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/min_mapped_reads.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -1241,7 +1241,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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2 changes: 1 addition & 1 deletion tests/nofasta.nf.test.snap
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"bioconductor-tximeta": "1.20.1"
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -1453,7 +1453,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/salmon.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -393,7 +393,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/skip_qc.nf.test.snap
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"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -187,7 +187,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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Expand Up @@ -136,7 +136,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/star_rsem.nf.test.snap
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Expand Up @@ -141,7 +141,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -1335,7 +1335,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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6 changes: 3 additions & 3 deletions tests/umi.nf.test.snap
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Expand Up @@ -144,7 +144,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -1637,7 +1637,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -2782,7 +2782,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0dev"
"nf-core/rnaseq": "v3.19.0"
}
},
[
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4 changes: 2 additions & 2 deletions workflows/rnaseq/assets/multiqc/multiqc_config.yml
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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev"
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.19.0"
target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how
to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output"
to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.19.0/docs/output"
target="_blank">documentation</a>.
report_section_order:
# Important checks and failures
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