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refactor(mqc): scope single-branch strand channels inside their if/else arm
The strand_*_merged + name_replacements channels were only consumed in the merged MULTIQC input build; strand_*_by_id + ch_per_sample_bundle only in the per-sample build. Move each into the branch that uses it so the reader doesn't have to jump out of the conditional to find a binding's only call site. The shared static config loads stay at top (both branches read them).
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Lines changed: 66 additions & 67 deletions

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  • subworkflows/local/multiqc_rnaseq

‎subworkflows/local/multiqc_rnaseq/main.nf‎

Lines changed: 66 additions & 67 deletions
Original file line numberDiff line numberDiff line change
@@ -88,69 +88,16 @@ workflow MULTIQC_RNASEQ {
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.map { f -> [[:], f] }
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//
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// Strandedness checks custom-content section. Two MultiQC subsections
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// (summary table + stacked composition bargraph) are rendered from
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// the same per-sample tuple, with header / pconfig / colour config
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// in the bundled YAML templates. The composition section inherits
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// `parent_*` from the summary section so the description lives in
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// one place.
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// Strandedness checks custom-content section. Two MultiQC
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// subsections (summary table + stacked composition bargraph) are
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// rendered from the same per-sample tuple, with header / pconfig
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// / colour config in the bundled YAML templates. The composition
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// section inherits `parent_*` from the summary section so the
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// description lives in one place.
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//
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def strand_summary_static = loadMultiqcAsset(strand_summary_asset)
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def strand_composition_static = loadMultiqcAsset(strand_composition_asset) + strand_summary_static.subMap(['parent_id', 'parent_name', 'parent_description'])
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// `.collect(flat: false)` is silent on an empty channel, so zero
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// strand rows -> no *_mqc.json emission -> MultiQC drops the section
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// cleanly.
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ch_strand_rows = ch_strand_data.collect(flat: false)
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ch_strand_summary_merged = ch_strand_rows
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.map { rows -> strandCheckSummaryYaml(strand_summary_static, rows) }
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.collectFile(name: 'strand_check_summary_mqc.json')
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.map { f -> [[:], f] }
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ch_strand_summary_by_id = ch_strand_data
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.collectFile { row ->
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[
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"${row[0].id}_strand_check_summary_mqc.json",
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strandCheckSummaryYaml(strand_summary_static, [row]),
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]
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}
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.map { f -> [f.baseName.replace('_strand_check_summary_mqc', ''), f] }
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ch_strand_composition_merged = ch_strand_rows
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.map { rows -> strandCheckCompositionYaml(strand_composition_static, rows) }
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.collectFile(name: 'strand_check_composition_mqc.json')
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.map { f -> [[:], f] }
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ch_strand_composition_by_id = ch_strand_data
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.collectFile { row ->
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[
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"${row[0].id}_strand_check_composition_mqc.json",
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strandCheckCompositionYaml(strand_composition_static, [row]),
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]
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}
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.map { f -> [f.baseName.replace('_strand_check_composition_mqc', ''), f] }
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//
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// Collapse the raw bundle with every per-sample contributor, one
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// `.join(remainder: true)` per stream. Each sample becomes
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// `[meta, [files]]`; missing streams show up as null entries that
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// are filtered out before MULTIQC sees them.
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//
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ch_per_sample_bundle = ch_per_sample_bundle_raw
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.join(ch_fail_trimmed_all.map { meta, f -> [meta.id, f] }, remainder: true)
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.join(ch_fail_mapped_all.map { meta, f -> [meta.id, f] }, remainder: true)
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.join(ch_strand_summary_by_id, remainder: true)
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.join(ch_strand_composition_by_id, remainder: true)
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.map { row ->
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[
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row[1],
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row.drop(2)
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.findAll { it != null }
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.collectMany { entry -> (entry instanceof List) ? entry : [entry] },
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]
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}
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// Per-run table_sample_merge config: only PE samples from the
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// samplesheet get their _1 / _2 rows grouped in the General Stats
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// table.
@@ -166,20 +113,18 @@ workflow MULTIQC_RNASEQ {
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.value(methodsDescriptionText(methods_description_yml))
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.collectFile(name: 'methods_description_mqc.yaml')
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// --replace-names TSV so MultiQC uses sample IDs rather than FASTQ basenames.
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ch_name_replacements = multiqcNameReplacements(ch_fastq)
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//
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// Two execution modes for MULTIQC:
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// - merged (default): one report covers the whole run.
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// - per-sample (--skip_quantification_merge): one report per
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// sample; workflow-level versions are replaced with a
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// pipeline-identity manifest so the report doesn't wait on the
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// global versions topic.
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// pipeline-identity manifest so the report doesn't wait on
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// the global versions topic.
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//
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// Each branch ends with a tuple matching the MULTIQC input contract
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// (id, files, configs, logo, replace_names, extra); the closure
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// below builds it so the branches stay focused on file assembly.
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// Each branch ends with a tuple matching the MULTIQC input
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// contract (id, files, configs, logo, replace_names, extra); the
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// closure below builds it so the branches stay focused on file
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// assembly.
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//
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def buildMultiqcInputTuple = { id, files, dynamic_config, replace_names = [] ->
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[
@@ -193,6 +138,42 @@ workflow MULTIQC_RNASEQ {
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}
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if (skip_quantification_merge) {
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ch_strand_summary_by_id = ch_strand_data
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.collectFile { row ->
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[
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"${row[0].id}_strand_check_summary_mqc.json",
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strandCheckSummaryYaml(strand_summary_static, [row]),
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]
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}
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.map { f -> [f.baseName.replace('_strand_check_summary_mqc', ''), f] }
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ch_strand_composition_by_id = ch_strand_data
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.collectFile { row ->
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[
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"${row[0].id}_strand_check_composition_mqc.json",
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strandCheckCompositionYaml(strand_composition_static, [row]),
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]
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}
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.map { f -> [f.baseName.replace('_strand_check_composition_mqc', ''), f] }
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// Collapse the raw bundle with every per-sample contributor,
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// one `.join(remainder: true)` per stream. Each sample becomes
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// `[meta, [files]]`; missing streams show up as null entries
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// that are filtered out before MULTIQC sees them.
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ch_per_sample_bundle = ch_per_sample_bundle_raw
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.join(ch_fail_trimmed_all.map { meta, f -> [meta.id, f] }, remainder: true)
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.join(ch_fail_mapped_all.map { meta, f -> [meta.id, f] }, remainder: true)
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.join(ch_strand_summary_by_id, remainder: true)
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.join(ch_strand_composition_by_id, remainder: true)
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.map { row ->
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[
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row[1],
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row.drop(2)
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.findAll { it != null }
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.collectMany { entry -> (entry instanceof List) ? entry : [entry] },
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]
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}
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ch_manifest_versions = channel.value(workflowVersionToYAML())
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.collectFile(name: 'nf_core_rnaseq_software_mqc_versions.yml')
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@@ -220,6 +201,24 @@ workflow MULTIQC_RNASEQ {
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)
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}
222203
} else {
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// `.collect(flat: false)` is silent on an empty channel, so
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// zero strand rows -> no *_mqc.json emission -> MultiQC drops
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// the section cleanly.
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ch_strand_rows = ch_strand_data.collect(flat: false)
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ch_strand_summary_merged = ch_strand_rows
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.map { rows -> strandCheckSummaryYaml(strand_summary_static, rows) }
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.collectFile(name: 'strand_check_summary_mqc.json')
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.map { f -> [[:], f] }
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ch_strand_composition_merged = ch_strand_rows
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.map { rows -> strandCheckCompositionYaml(strand_composition_static, rows) }
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.collectFile(name: 'strand_check_composition_mqc.json')
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.map { f -> [[:], f] }
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// --replace-names TSV so MultiQC uses sample IDs rather than FASTQ basenames.
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ch_name_replacements = multiqcNameReplacements(ch_fastq)
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// `multiqc_report` is a sentinel meta.id used by
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// conf/modules/multiqc.config to pick the merged output path.
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ch_multiqc_files_merged = ch_multiqc_files

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