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Fixes parametrization of SUBREAD_FEATURECOUNTS depending on meta.single_read #453

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Mar 12, 2025
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Fixes parametrization of SUBREAD_FEATURECOUNTS depending on meta.single_read #453

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d9d5e97
Pass map.single_read to feature counts
JoseEspinosa Mar 11, 2025
412e20e
Update changelog
JoseEspinosa Mar 11, 2025
f5e8f1d
Make lint happy
JoseEspinosa Mar 11, 2025
5483399
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JoseEspinosa Mar 11, 2025
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -7,11 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1
- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to `1.25.1`.
- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
- Updated pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0)
- Updated pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0).
- [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.

### Parameters

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4 changes: 2 additions & 2 deletions subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
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Expand Up @@ -90,8 +90,8 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
}
.join(ch_bams)
.map {
antibody, meta, saf, bams ->
[ meta, bams.flatten().sort(), saf ]
antibody, meta, saf, bams, meta_single_end ->
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the comment of ch_bams at line 15 has to be updated, it confused me about the content of this channel here

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Good spot!

[ meta + meta_single_end, bams.flatten().sort(), saf ]
}
.set { ch_bam_saf }

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8 changes: 6 additions & 2 deletions workflows/chipseq.nf
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Expand Up @@ -130,7 +130,6 @@ workflow CHIPSEQ {
)
ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions)


//
// SUBWORKFLOW: Alignment with BWA & BAM QC
//
Expand Down Expand Up @@ -474,9 +473,14 @@ workflow CHIPSEQ {
ch_ip_control_bam
.map {
meta, ip_bam, control_bam ->
[ meta.antibody, ip_bam ]
[ meta.antibody, meta.single_end, ip_bam ]
}
.groupTuple()
.map {
antibody, single_end, ip_bams ->
def single_end_map = single_end.unique().size() == 1 ? [single_end: single_end[0]] : false
[ antibody, ip_bams, single_end_map ]
}
.set { ch_antibody_bams }

BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 (
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