feat: add topic version emission to quant-related modules#10931
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pinin4fjords merged 1 commit intomasterfrom Mar 17, 2026
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feat: add topic version emission to quant-related modules#10931pinin4fjords merged 1 commit intomasterfrom
pinin4fjords merged 1 commit intomasterfrom
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Convert custom/tx2gene, tximeta/tximport, and summarizedexperiment/summarizedexperiment to emit versions via topic channels, enabling automatic version collection in downstream subworkflows. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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| output: | ||
| tuple val(meta), path("*tx2gene.tsv"), emit: tx2gene | ||
| path "versions.yml" , emit: versions | ||
| path "versions.yml" , emit: versions, topic: versions |
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| path "versions.yml" , emit: versions, topic: versions | |
| path "versions.yml" , emit: versions_tx2gene, topic: versions |
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Nevermind, we agreed on a decision.
So versions.yml emitted via template are sent to the versions topics and emitted via versions only.
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Thanks @maxulysse ! |
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…view issues - Remove ch_versions collection and versions emit from all three quant subworkflows (versions now handled via topic channels from #10931) - Remove `def` keyword from channel variable declarations for consistency - Add comment explaining why .first() is safe for tx2gene discovery Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Add an optional skip_merge boolean input to quant_tximport_summarizedexperiment, quantify_pseudo_alignment, and quantify_rsem. When true: - tximport runs per-sample (preserving input meta) instead of collecting all - SummarizedExperiment creation is skipped - RSEM merge counts are skipped (quantify_rsem only) When false (default), behavior is identical to before. Additional improvements made alongside this feature: - CUSTOM_TX2GENE now uses .first() unconditionally for transcript ID discovery, since it only ever reads one sample's files. This assumes all samples were quantified against the same transcriptome (documented in meta.yml). If mixed-transcriptome support is needed in future, tx2gene would need to run independently per sample. - Version collection removed from all three subworkflows. The underlying modules now emit via topic channels (nf-core#10931), so manual ch_versions plumbing is no longer needed. Used by nf-core/rnaseq --skip_quantification_merge (nf-core/rnaseq#1744). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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#10928) Add an optional skip_merge boolean input to quant_tximport_summarizedexperiment, quantify_pseudo_alignment, and quantify_rsem. When true: - tximport runs per-sample (preserving input meta) instead of collecting all - SummarizedExperiment creation is skipped - RSEM merge counts are skipped (quantify_rsem only) When false (default), behavior is identical to before. Additional improvements made alongside this feature: - CUSTOM_TX2GENE now uses .first() unconditionally for transcript ID discovery, since it only ever reads one sample's files. This assumes all samples were quantified against the same transcriptome (documented in meta.yml). If mixed-transcriptome support is needed in future, tx2gene would need to run independently per sample. - Version collection removed from all three subworkflows. The underlying modules now emit via topic channels (#10931), so manual ch_versions plumbing is no longer needed. Used by nf-core/rnaseq --skip_quantification_merge (nf-core/rnaseq#1744). Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
custom/tx2gene,tximeta/tximport, andsummarizedexperiment/summarizedexperimentto emit versions viatopic: versionschannelstopicssection and updated version output descriptionsThis enables downstream subworkflows (e.g.
quant_tximport_summarizedexperiment) to collect versions automatically via topic channels instead of manualch_versions.mix(), which is needed for conditional execution paths like #10928.Follows the pattern I observed in #10873 for templated modules.
Test plan
process.out.versionsstill works in tests (emit is preserved alongside topic)🤖 Generated with Claude Code