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Try fix for damageprofiler sometimes needing a fai file #929

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Merged
jfy133 merged 3 commits into from
Nov 2, 2022
Merged

Try fix for damageprofiler sometimes needing a fai file #929

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dab6cee
Try fix for damageprofiler sometimes needing a fai file
jfy133 Oct 24, 2022
801a900
Update CHANGELOG.md
jfy133 Oct 24, 2022
7c848e4
Merge branch 'patch' into patch-damageprofiler-fai
jfy133 Nov 2, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Changed endors.py license from GPL to MIT (by @aidaanva)
- Removed erroneous R2 in single-end example in input TSV of usage docs (by @aidaanva)
- [#928](https://github.com/nf-core/eager/issues/928) Fixed read group incompatibility by re-adding picard AddOrReplaceReadGroups for MultiVCFAnalyzer (♥ to @aidaanva, @meganemichel for reporting)
- Fixed edge case of DamageProfiler occasionally requiring FASTA index (♥ to @asmaa-a-abdelwahab for reporting)

### `Dependencies`

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3 changes: 2 additions & 1 deletion main.nf
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Expand Up @@ -578,7 +578,7 @@ process makeFastaIndex {
}

ch_fai_for_skipfastaindexing.mix(ch_fasta_faidx_index)
.into { ch_fai_for_ug; ch_fai_for_hc; ch_fai_for_freebayes; ch_fai_for_pileupcaller; ch_fai_for_angsd }
.into { ch_fai_for_damageprofiler; ch_fai_for_ug; ch_fai_for_hc; ch_fai_for_freebayes; ch_fai_for_pileupcaller; ch_fai_for_angsd }

// Stage dict index file if supplied, else load it into the channel

Expand Down Expand Up @@ -2091,6 +2091,7 @@ process damageprofiler {
input:
tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_damageprofiler
file fasta from ch_fasta_for_damageprofiler.collect()
file fai from ch_fai_for_damageprofiler.collect()

output:
tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${base}/*.txt") optional true
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