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Skip RUNDIRPARSER if no rundir information is available #167

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Merged
maxulysse merged 6 commits into from
Feb 9, 2026
Merged

Skip RUNDIRPARSER if no rundir information is available #167

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cfd4a8d
Skip RUNDIRPARSER if no rundir information is available
matrulda Jan 19, 2026
6e56eab
Add 167 to changelog
matrulda Jan 19, 2026
960728a
Add test for no rundir information scenario
matrulda Jan 19, 2026
e535dc1
Add note about RUNDIRPARSER being skipped when not using rundir
matrulda Jan 20, 2026
749aee2
pre-commit fix
matrulda Jan 20, 2026
d080687
Write warning if rundir is missing for a sample
matrulda Feb 6, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -49,6 +49,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#150](https://github.com/nf-core/seqinspector/pull/150) Fix pipeline linting issues
- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
- [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available

### `Changed`

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3 changes: 3 additions & 0 deletions workflows/seqinspector.nf
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Expand Up @@ -67,6 +67,7 @@ workflow SEQINSPECTOR {
// From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
// --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
ch_rundir = ch_samplesheet
.filter { meta, _reads -> meta.rundir.size() > 0 }
.map { meta, _reads -> [meta.rundir, meta] }
.groupTuple()
.map { rundir, metas ->
Expand All @@ -82,6 +83,8 @@ workflow SEQINSPECTOR {
[dir_meta, rundir]
}

ch_rundir.ifEmpty { log.warn "No samples with rundir found, skipping RUNDIRPARSER" }

RUNDIRPARSER(ch_rundir)

ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
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