Dev#161
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initial syntax changes and bulk modules update
Document tuple structures for all major channels in lrsomatic.nf, tumor_normal_happhase.nf, tumor_only_happhase.nf, and prepare_reference_files.nf using [meta, elem1, elem2] style comments. Replaces verbose multi-line comments with consistent single-line format and fixes one mislabelled comment (tumor_bams_phasedvcf was labelled as tumor_bams_germlinevcf). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
add skip_m6a param
… into template_update
template update
Bug fix consensus
updated wakhan
update default
ljwharbers
approved these changes
Jun 3, 2026
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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).