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fix(fastq_qc_trim_filter_setstrandedness): expose fastp's merged reads #12895

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Merged
pinin4fjords merged 2 commits into from
Sep 7, 2026
Merged

fix(fastq_qc_trim_filter_setstrandedness): expose fastp's merged reads #12895

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6b8beb6
fix(fastq_qc_trim_filter_setstrandedness): expose fastp's merged read…
pinin4fjords Sep 6, 2026
51fd4a4
Merge branch 'master' into fix/fastq-qc-trim-filter-fastp-merge
jonasscheid Sep 7, 2026
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3 changes: 3 additions & 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 @@ -132,6 +132,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {

ch_filtered_reads = channel.empty()
ch_trim_read_count = channel.empty()
ch_trim_reads_merged = channel.empty()
ch_multiqc_files = channel.empty()
ch_lint_log_raw = channel.empty()
ch_lint_log_trimmed = channel.empty()
Expand Down Expand Up @@ -240,6 +241,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
)
ch_filtered_reads = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads
ch_trim_read_count = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_read_count
ch_trim_reads_merged = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_merged

// Capture individual outputs for workflow outputs
ch_fastqc_raw_html = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_html
Expand Down Expand Up @@ -433,6 +435,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
reads_cat = ch_reads_cat
reads_trimmed = ch_reads_trimmed
trim_read_count = ch_trim_read_count
trim_reads_merged = ch_trim_reads_merged
multiqc_files = ch_multiqc_files.transpose()

// Individual outputs for workflow outputs
Expand Down
9 changes: 9 additions & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml
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Expand Up @@ -171,6 +171,15 @@ output:
Number of reads remaining after trimming for all input samples.

Structure: [ val(meta), val(count) ]
- trim_reads_merged:
type: file
description: |
fastp's merged overlapping read pairs, produced only when `trimmer == 'fastp'` and
`fastp_merge == true`. Empty otherwise. These reads are excluded from `reads`;
callers that want to use them downstream must consume this channel separately.

Structure: [ val(meta), path(reads) ]
pattern: "*.merged.fastq.gz"
- multiqc_files:
type: file
description: |
Expand Down
1 change: 1 addition & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
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Expand Up @@ -122,6 +122,7 @@ nextflow_workflow {
{ assert pelines2.size() == 4508 },
{ assert workflow.out.trim_read_count[0][1] == 3022 },
{ assert sortmernaRrnaCount == 20 }, // 10 pairs = 20 individual reads (100% detection)
{ assert path(workflow.out.trim_reads_merged[0][1]).linesGzip.size() == 3022 * 4 }, // fastp's merged overlapping read pairs, excluded from `reads`
{ assert snapshot(
pelines1.join('\n').md5(),
pelines2.join('\n').md5(),
Expand Down