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Add haplotype DMR (differential methylation region) calling - #204

Merged

ljwharbers merged 30 commits into

IntGenomicsLab:devfrom

YannVRB:add-dmr-haplotypes

Oct 27, 2026

Merged

Add haplotype DMR (differential methylation region) calling#204
ljwharbers merged 30 commits into
IntGenomicsLab:devfrom
YannVRB:add-dmr-haplotypes

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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  3a7b8f0
- Add haplotype DMR subworkflow, local modules, and vendored nf-core dependencies
  
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  fdc73a6
- 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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  dd729e5
- 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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  28a6e88
- DMR_NEAREST_GENE: use bedtools closest -D b, not -D a
  
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  41446be
- Add real subworkflow-level nf-test for DMR, tagged small
  
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  1ae56c7
Commits on Sep 30, 2026
- MODKIT_DMR: avoid rebuilding fai every run, use the same patched modkit as pileup
  
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  28e72e9
- Publish MODKIT_DMR's log for debugging
  
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  7644f58
Commits on Oct 13, 2026
- Add missing trailing newline to modules.json
  
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  b8e4e96
Commits on Oct 14, 2026
- Merge origin/dev into add-dmr-haplotypes
  
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  6d10044
Commits on Oct 15, 2026
- Re-trigger CI (modkit/dmr fork branch restored)
  
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  c151300
- Disable prek-action caching to avoid corrupted hook cache
  
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  b9c0413
- Replace prek-action with plain pre-commit in linting CI
  
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  51d1d20
- Apply prettier formatting to modules.json
  
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  bc36ae0
- Re-trigger CI (check SAVANA breakpoints_double.csv determinism)
  
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  938da2e
- Update stale breakpoints_double.csv md5s in default pipeline snapshot
  
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  b7e7382
Commits on Oct 17, 2026
- Auto-include 5hmC in MODKIT_PILEUP args when DMR will run
  
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  515b522
- Re-point modkit/dmr at nf-core/modules now that #13021 merged
  
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  f723a11
- Add usage/output docs and CHANGELOG entry for haplotype DMR
  
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  2476e53
Commits on Oct 26, 2026
- Merge origin/dev into add-dmr-haplotypes
  
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  5e71311
- DMR: gate the 5hmC append on DMR references, document its effect on published pileups
  
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  1e2bbda
- DMR: resolve the CpG-island/gene BEDs into locals so the genome defaults apply
  
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  843ec83
Commits on Oct 27, 2026
- DMR: skip samples with no CpG island covered in both haplotypes
  
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  ed5e7e2
- modkit/dmr: fit the module test to the patched pileup, re-record snapshot
  
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  8ebea39
- DMR: trim verbose inline comments
  
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  3890431
- SIGPROFILER_VERIFY: print the error before the checksum table
  
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  ae8bccc

Commits

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Commits on Sep 28, 2026

Commits on Sep 30, 2026

Commits on Oct 13, 2026

Commits on Oct 14, 2026

Commits on Oct 15, 2026

Commits on Oct 17, 2026

Commits on Oct 26, 2026

Commits on Oct 27, 2026