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Add new nf-core module wrapping `modkit validate`, which benchmarks modified-base calls in one or more mod-BAMs against paired ground-truth BED files and emits a tab-separated summary of correct / incorrect / filtered calls per class. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Adds a new nf-core module wrapping `modkit validate`, which benchmarks base-modification calls in one or more mod-BAMs against paired ground-truth BED files and emits a tab-separated summary of correct / incorrect / filtered calls per class.
The module accepts paired lists of BAMs and truth-BEDs (1:1 by list index) and forwards each pair as a repeated `--bam-and-bed ` argument to modkit.
Why
`modkit validate` is the only canonical way to benchmark ONT methylation-calling accuracy against ground truth and is not currently in nf-core/modules. It's used to compare modkit pileup thresholds, evaluate basecaller-model upgrades, and assess spike-in control performance.
Test data — stub only
`modkit validate` requires a BAM paired with a ground-truth BED whose name column is a single-letter modified-base code (`m`, `h`, ...) or `-` for a canonical reference position. The public nf-core test-datasets modules branch doesn't ship such a BED. Committed test is stub-only with a placeholder `genome.bed` for staging; the meta.yml documents the truth-BED contract for downstream users. Happy to contribute a small curated truth BED to nf-core/test-datasets in a follow-up.
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