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Slight fixes for rnaseq preprocessing #1382

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Merged
pinin4fjords merged 6 commits into from
Sep 16, 2024
Merged

Slight fixes for rnaseq preprocessing #1382

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262672c
slight fixes for rnaseq prepro
pinin4fjords Sep 13, 2024
3701544
Remove chunk duplicated from subworkflow
pinin4fjords Sep 13, 2024
5c6982c
Try from branch
pinin4fjords Sep 13, 2024
8244d50
Merge branch 'dev' into rnaseq_propro_trimfail_fix
pinin4fjords Sep 16, 2024
3e9af61
install subworkflow from master
pinin4fjords Sep 16, 2024
5703690
Update changelog
pinin4fjords Sep 16, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
- [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing

## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -325,7 +325,7 @@
},
"fastq_qc_trim_filter_setstrandedness": {
"branch": "master",
"git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0",
"git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af",
"installed_by": ["subworkflows"]
},
"fastq_subsample_fq_salmon": {
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
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19 changes: 0 additions & 19 deletions workflows/rnaseq/main.nf
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Expand Up @@ -167,25 +167,6 @@ workflow RNASEQ {
meta, num_reads ->
return [ meta.id, num_reads > params.min_trimmed_reads.toFloat() ]
}
//
// Get list of samples that failed trimming threshold for MultiQC report
//
ch_trim_read_count
.map {
meta, num_reads ->
if (num_reads <= params.min_trimmed_reads.toFloat()) {
return [ "$meta.id\t$num_reads" ]
}
}
.collect()
.map {
tsv_data ->
def header = ["Sample", "Reads after trimming"]
sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header)
}
.set { ch_fail_trimming_multiqc }

ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv'))

//
// SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon
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