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Fix bigwig strand labeling for reverse-stranded libraries #1620

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Merged
pinin4fjords merged 4 commits into from
Nov 25, 2025
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Merged

Fix bigwig strand labeling for reverse-stranded libraries #1620

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7dd436c
Fix bigwig strand labeling for reverse-stranded libraries
pinin4fjords Nov 14, 2025
8267cc8
Update CHANGELOG.md
pinin4fjords Nov 14, 2025
fbf71f8
Add comment about conditional strand parameters
pinin4fjords Nov 14, 2025
94a7c43
Merge branch 'dev' into fix-bigwig-reverse-strand-labeling
pinin4fjords Nov 25, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,11 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
Special thanks to the following for their contributions to the release:

- [Elad Herzog](https://github.com/EladH1)
- [Emily Miyoshi](https://github.com/emilymiyoshi)

### Enhancements and fixes

- [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
- [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
- [PR #1620](https://github.com/nf-core/rnaseq/pull/1620) - Fix bigwig strand labeling for reverse-stranded libraries ([#1591](https://github.com/nf-core/rnaseq/issues/1591))

## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18

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1 change: 1 addition & 0 deletions workflows/rnaseq/main.nf
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Expand Up @@ -499,6 +499,7 @@ workflow RNASEQ {

//
// MODULE: Genome-wide coverage with BEDTools
// Note: Strand parameters are conditional on library strandedness (see nextflow.config)
//
if (!params.skip_bigwig) {

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4 changes: 2 additions & 2 deletions workflows/rnaseq/nextflow.config
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Expand Up @@ -335,15 +335,15 @@ if (!params.skip_bigwig) {
process {
withName: 'BEDTOOLS_GENOMECOV_FW' {
ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.reverse' : meta.id + '.forward' }
ext.args = '-split -du -strand + -bg'
ext.args = { meta.strandedness == 'reverse' ? '-split -du -strand - -bg' : '-split -du -strand + -bg' }
publishDir = [
enabled: false
]
}

withName: 'BEDTOOLS_GENOMECOV_REV' {
ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.forward' : meta.id + '.reverse' }
ext.args = '-split -du -strand - -bg'
ext.args = { meta.strandedness == 'reverse' ? '-split -du -strand + -bg' : '-split -du -strand - -bg' }
publishDir = [
enabled: false
]
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