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Add new nf-core module wrapping `modkit extract calls`, which emits a per-read per-position table of base modification calls using the same pass/fail thresholding as `modkit pileup`. Complementary to `modkit/extract/full` (raw probabilities): this module emits the thresholded categorical decisions. Useful for per-read downstream analysis such as allele-specific methylation and methylation-aware phasing. 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 calls`, which produces a per-read per-position table of base-modification calls (pass / fail / filtered, with the called base) using the same thresholding algorithm as `modkit pileup`.
Complementary to `modkit/extract/full`: `extract calls` emits the thresholded categorical decision per site per read, while `extract full` emits the underlying probabilities.
The module auto-detects `--bgzf` in `ext.args` and adjusts the output filename suffix accordingly.
Why
`modkit extract calls` is the go-to tool for per-read allele-specific methylation, methylation-aware phasing validation, and read-level QC where you want the same thresholded labels as the pileup output but at read level rather than site level.
Test data
Uses the existing `test.sorted.phased.bam` from nf-core/test-datasets (modules branch). No new test data required.
🤖 Generated with Claude Code