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Add new nf-core module wrapping `modkit entropy`, which computes methylation entropy over genomic windows from one or more mod-BAMs. Supports an optional BED of regions for per-region descriptive statistics; emits a genome-wide BED otherwise. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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--cpgmode).topic: versions.process_high).Summary
Adds a new nf-core module wrapping `modkit entropy`, which computes methylation entropy over genomic windows from one or more mod-BAMs. Entropy is a per-window measure of the diversity of methylation patterns across reads covering the window and is complementary to mean methylation.
The module supports modkit's file-vs-directory output dichotomy: when `--regions` is supplied (either via `ext.args` or the third input channel), modkit writes per-region BED / bedgraph / TSV into a directory (emitted via `regions_bed`, `bedgraph`, `tsv` outputs); otherwise a single genome-wide BED is produced (emitted via `bed`).
Accepts multiple input BAMs (passed as repeated `--in-bam`) for multi-sample entropy.
Why
`modkit entropy` is the canonical tool for quantifying methylation heterogeneity in ONT methylation data and is not currently in nf-core/modules. It complements the existing `modkit/pileup` (mean methylation) for heterogeneity-aware analyses.
Test data
Uses the existing `test.sorted.phased.bam` from nf-core/test-datasets (modules branch, `genomics/homo_sapiens/nanopore/bam/`). No new test data required.
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