feat: add nf-core-compatible bigWig coverage tracks#114
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Implement bedtools genomecov-equivalent coverage accumulation in the
existing BAM streaming pass and write bigWig files via bigtools.
Produces nf-core/rnaseq-compatible outputs:
- {sample}.bigWig (combined, -split -bg)
- {sample}.forward/reverse.bigWig for stranded libraries (-split -du -strand)
Validated against bedtools genomecov + UCSC bedClip/bedGraphToBigWig in
integration tests.
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Add a dedicated bigWig docs page and update README, AGENTS.md, CONTRIBUTING.md, getting-started guides, credits, CLI/config references, benchmark details, and library doc comments to describe nf-core/rnaseq- compatible genome coverage track output. Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
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Summary
Implements genome-wide bigWig coverage tracks in the existing
rustqc rnaBAM streaming pass, matching nf-core/rnaseq parameters (bedtools genomecov -split, optional-du/-strand, UCSCbedClipsemantics).Closes #112.
Changes
src/rna/bigwig/module: coverage accumulation, bedGraph clipping, bigWig writing viabigtoolscount_reads()read loop andmain.rsoutput underbigwig/rna.bigwig.enabled(defaulttrue)Output files
{sample}.bigWig— combined track (all libraries){sample}.forward.bigWig/{sample}.reverse.bigWig— per-strand tracks (stranded libraries only)Validation
genomecovv2.31.1 exactly (738/738 intervals in integration tests).bigWigfiles are not bit-identical to UCSCbedGraphToBigWig(different encoder), but decode to the same coverageFollow-ups
bedGraphToBigWigsubprocess for bit-identical binaries if required