fix(fastq_qc_trim_filter_setstrandedness): expose fastp's merged reads - #12895
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pinin4fjords merged 2 commits intoSep 7, 2026
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…s instead of silently dropping them
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jonasscheid
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Sep 7, 2026
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Thanks @jonasscheid ! |
pinin4fjords
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…mits fastq_qc_trim_filter_setstrandedness -> 0853b48c (nf-core/modules#12895) orftable_fasta_gtf_buildorfcatalogue -> 7baf88e0 (nf-core/modules#12896) Both PRs are merged. Synced modules.json and the two changed files to their exact merge-commit content (not current master HEAD, to avoid pulling in unrelated later changes). orftable_fasta_gtf_buildorfcatalogue was already byte-identical (riboseq's copy already matched). Resolves the check_local_copy lint failures that were expected pending these merges.
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Summary
FASTQ_FASTQC_UMITOOLS_FASTPalready emits fastp's merged overlapping read pairs (FASTP.out.reads_merged), butFASTQ_QC_TRIM_FILTER_SETSTRANDEDNESSnever captured or re-emitted that channel. Any caller enablingfastp_mergegets its merged reads silently dropped, with no output, no error, and no way to consume them downstream.What changed
ch_trim_reads_merged, captured fromFASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_mergedin the fastp branch, initialised tochannel.empty()elsewhere.trim_reads_mergedsubworkflow output.meta.yml.homo_sapiens paired-end [fastq] fastp sortmernatest (which already runs withfastp_merge = true) confirming the merged-reads file is non-empty with the expected read count.This is purely additive — no existing output changes shape, so downstream pipelines that don't consume the new output are unaffected.
Found while reviewing nf-core/riboseq's v2.0.0 release PR, which vendors this subworkflow and hits the bug via
--fastp_merge.