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Add new nf-core module wrapping `modkit extract full`, which transforms the MM/ML tags in a modBAM into a tab-separated per-read-per-position probability table. Output can be BGZF-compressed via `--bgzf` in `ext.args`. Useful for downstream custom filtering, plotting, and ML training on read-level methylation probabilities. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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PR checklist
Summary
Adds a new nf-core module wrapping `modkit extract full`, which transforms the MM/ML tags in a modBAM into a tab-separated per-read-per-position probability table. Emits one row for every modified-base probability call in every read.
The module auto-detects `--bgzf` in `ext.args` and adjusts the output filename suffix accordingly (`.tsv` vs `.tsv.gz`), so users don't get a misleading extension when enabling compression.
Why
`modkit extract full` is the source of truth for read-level methylation probabilities and is essential for custom downstream filtering, phased methylation plots, and ML training on raw probability distributions. Paired with `modkit extract calls` (companion PR) which emits thresholded categorical calls.
Test data
Uses the existing `test.sorted.phased.bam` from nf-core/test-datasets (modules branch). No new test data required.
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