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IntGenomicsLab
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Add haplotype DMR (differential methylation region) calling
- #204
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Add haplotype DMR (differential methylation region) calling
#204
YannVRB
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YannVRB:add-dmr-haplotypes
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Commits on Sep 23, 2026
Vendor modkit/dmr module ahead of upstream merge
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Add DMR params and reference config
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Add haplotype DMR subworkflow, local modules, and vendored nf-core dependencies
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Point igenomes.config TODOs at the now-open reference-fixtures PR
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Commits on Sep 24, 2026
Re-point DMR reference URLs at the now-merged IntGenomicsLab/test-datasets
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Commits on Sep 28, 2026
Re-vendor modkit/dmr from current upstream head; drop unused bedtools modules
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Declare dmr_cpg_islands_bed/dmr_gencode_gene_bed; skip DMR gracefully when unset
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DMR_HAPLOTYPE_REGIONS: query via tabix -R, add a minimum-coverage threshold
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DMR_NEAREST_GENE: use bedtools closest -D b, not -D a
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Add real subworkflow-level nf-test for DMR, tagged small
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Commits on Sep 30, 2026
MODKIT_DMR: avoid rebuilding fai every run, use the same patched modkit as pileup
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