feat: Add emit statements to support Nextflow workflow outputs #9765
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Add individual output channel emits to subworkflows to support the new Nextflow workflow outputs syntax (25.10+). These changes allow pipelines to publish outputs centrally rather than via publishDir directives. Updated subworkflows: - bam_dedup_stats_samtools_umitools: add tsv_edit_distance, tsv_per_umi, tsv_umi_per_position emits - bam_dedup_umi: add tsv_* emits when using umitools - fastq_fastqc_umitools_fastp: add umi_reads emit - fastq_fastqc_umitools_trimgalore: add umi_reads emit - fastq_qc_trim_filter_setstrandedness: add individual output channels for all QC/trim/filter outputs - fastq_remove_rrna: add individual output channels for each tool - quantify_pseudo_alignment: add tx2gene emit Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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The lint_log emit was split into individual channels (lint_log_raw, lint_log_trimmed, lint_log_bbsplit, lint_log_ribo) for workflow outputs. Update test assertions to use lint_log_ribo directly. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
SPPearce
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Jan 23, 2026
subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap
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Several null.tx2gene.tsv files being generated now, when they weren't called that before?
Synced from nf-core/rnaseq#1679 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add process configs for CUSTOM_TX2GENE and TXIMETA_TXIMPORT to set proper file prefixes when meta is empty. Also sync SALMON_QUANT and KALLISTO_QUANT configs from nf-core/rnaseq#1679. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add additional emit channels to expose intermediate BAM files from the transcriptome deduplication pipeline, enabling workflow outputs support. New emits: - transcriptome_dedup_bam: BAM after deduplication, before name sort - transcriptome_sorted_bam: name-sorted BAM - transcriptome_sorted_bam_bai: coordinate-sorted dedup index - transcriptome_filtered_bam: paired-end filtered BAM Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add CUSTOM_TX2GENE and TXIMETA_TXIMPORT process configs to the test nextflow.config to fix null.tx2gene.tsv filename issue. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update stub to respect task.ext.prefix configuration, falling back to meta.id. This ensures stub tests produce consistent output filenames with the real script. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Align emit statements consistently in bam_dedup_umi and fastq_qc_trim_filter_setstrandedness subworkflows. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Failures are just singularity timeouts... |
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Summary
Add individual output channel emits to subworkflows to support the new Nextflow workflow outputs syntax (25.10+). These changes allow pipelines to publish outputs centrally rather than via
publishDirdirectives.This PR ports the subworkflow changes from nf-core/rnaseq#1679 to the modules repo.
Changes
Updated subworkflows:
tsv_edit_distance,tsv_per_umi,tsv_umi_per_positiontsv_edit_distance,tsv_per_umi,tsv_umi_per_position(when using umitools)umi_readsumi_readssortmerna_log,ribodetector_log,seqkit_stats,bowtie2_log,bowtie2_index,seqkit_prefixed,seqkit_convertedtx2geneTest plan
snapshot(workflow.out):🤖 Generated with Claude Code