Output syntax Migration#2066
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Test running successfully - The pipeline launched with the new workflow outputs structure:
- publish: block in entry workflow ✅
- output {} block with dynamic paths ✅
- workflow.output.mode = 'copy' in config ✅
What this means:
- The new workflow outputs feature is additive - it publishes outputs through the new system
- The old publishDir system is still active in the configs
- Both systems will publish outputs (some duplication expected until publishDir is removed)
Workflow outputs infrastructure added:
- publish: block in entry workflow (main.nf)
- output {} block with dynamic paths
- workflow.output.mode = 'copy' in nextflow.config
Channel emission chain established:
- fastq_preprocess_gatk → SAREK workflow → NFCORE_SAREK entry workflow
- Add markduplicates_metrics output channel - Add strelka genome VCF/TBI output channels (separate from variant VCF) - Thread all new channels through workflow hierarchy - Update nf-test snapshots with new outputs
- Add MD QC channel propagation through workflow hierarchy - Fix strelka genome VCF TBI output in bam_variant_calling_single_strelka - Fix mosdepth stub file naming to include .mosdepth. infix - Update test snapshot with consistent naming
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.3.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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maxulysse
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Jan 15, 2026
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let's not commit this whole folder please
maxulysse
reviewed
Jan 15, 2026
| // Workflow outputs configuration | ||
| workflow { | ||
| output { | ||
| mode = 'copy' |
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Suggested change
| mode = 'copy' | |
| mode = params.publish_dir_mode |
maxulysse
reviewed
Jan 15, 2026
| workflow { | ||
| output { | ||
| mode = 'copy' | ||
| overwrite = true |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).