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Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow #9559

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pinin4fjords merged 1 commit into from
Dec 11, 2025
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Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow #9559

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1 change: 1 addition & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
BBMAP_BBSPLIT.out.primary_fastq.set { ch_filtered_reads }

ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBSPLIT.out.stats)
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@FriederikeHanssen FriederikeHanssen Dec 11, 2025

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are you stripping the meta later? I ran into that on sarek when adding it here

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@pinin4fjords pinin4fjords Dec 11, 2025

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yep!

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@pinin4fjords pinin4fjords Dec 11, 2025

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modules/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

Line 345 in 9a571f1

multiqc_files = ch_multiqc_files.transpose().map { it[1] }


if (!skip_linting) {
FQ_LINT_AFTER_BBSPLIT(
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