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Merge branch 'dev' into fix_r_checknames_from_dev
2 parents 6f4518c + 13f5dcd commit fef8aa4

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‎.github/workflows/nf-test.yml‎

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name: Run nf-test
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on:
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pull_request:
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paths-ignore:
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- "docs/**"
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- "**/meta.yml"
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- "**/*.md"
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- "**/*.png"
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- "**/*.svg"
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release:
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types: [published]
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workflow_dispatch:
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fi
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confirm-pass:
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needs: [nf-test]
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needs: [nf-test-changes, nf-test]
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if: always()
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runs-on: # use self-hosted runners
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- runs-on=${{ github.run_id }}-confirm-pass
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- name: debug-print
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if: always()
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run: |
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echo "::group::DEBUG: `needs` Contents"
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echo "::group::DEBUG: needs Contents"
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echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
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echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
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echo "::endgroup::"

‎.nf-core.yml‎

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lint:
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actions_nf_test: false
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files_exist:
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- conf/modules.config
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files_unchanged:

‎CHANGELOG.md‎

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Special thanks to the following for their contributions to the release:
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- [Elad Herzog](https://github.com/EladH1)
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- [Emily Miyoshi](https://github.com/emilymiyoshi)
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### Enhancements and fixes
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- [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
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- [PR #1618](https://github.com/nf-core/rnaseq/pull/1618) - Fix CI: Ensure confirm-pass job runs for markdown-only PRs
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- [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
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- [PR #1622](https://github.com/nf-core/rnaseq/pull/1622) - Update tximeta/tximport module to fix sample name mangling
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- [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))
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- [PR #1621](https://github.com/nf-core/rnaseq/pull/1621) - Optimize qualimap performance with multi-threaded name sorting
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## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
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‎modules/nf-core/qualimap/rnaseq/nextflow.config‎

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‎tests/bam_input.nf.test.snap‎

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{
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"BAM input for Salmon": {
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"content": [
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{
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"BBMAP_BBSPLIT": {
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"bbmap": 39.18
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"SAMTOOLS_INDEX": {
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"samtools": 1.21
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},
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"SAMTOOLS_SORT_QUALIMAP": {
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},
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"SAMTOOLS_STATS": {
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},
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},
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"BAM input for RSEM": {
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"BBMAP_BBSPLIT": {
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"SAMTOOLS_INDEX": {
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"SAMTOOLS_SORT_QUALIMAP": {
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},
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‎tests/default.nf.test.snap‎

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},
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"Params: default": {
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"content": [
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{
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"BBMAP_BBSPLIT": {
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"SAMTOOLS_SORT": {
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"SAMTOOLS_SORT_QUALIMAP": {
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},
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"SAMTOOLS_STATS": {
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‎tests/featurecounts_group_type.nf.test.snap‎

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"Params: --featurecounts_group_type false": {
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"SAMTOOLS_SORT": {
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"SAMTOOLS_SORT_QUALIMAP": {
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‎tests/hisat2.nf.test.snap‎

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},
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"Params: --aligner hisat2": {
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"BBMAP_BBSPLIT": {
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"SAMTOOLS_SORT": {
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"SAMTOOLS_SORT_QUALIMAP": {
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‎tests/min_mapped_reads.nf.test.snap‎

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{
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"Params: --min_mapped_reads 90": {
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‎tests/remove_ribo_rna.nf.test.snap‎

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{
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"Params: --remove_ribo_rna": {
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},
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"SAMTOOLS_STATS": {
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},

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