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fix(modkit): patched modkit 0.6.4 for PacBio 5mC+5hmC reads, 5mC-CpG pileup defaults and --modkit_phased option - #188

Merged

AmberVerhasselt merged 14 commits into

devfrom

fix/modkit-pacbio-container

Sep 14, 2026

Merged

fix(modkit): patched modkit 0.6.4 for PacBio 5mC+5hmC reads, 5mC-CpG pileup defaults and --modkit_phased option#188
AmberVerhasselt merged 14 commits into
devfrom
fix/modkit-pacbio-container

Commits on Sep 2, 2026
- fix(modkit): run a patched modkit 0.6.4 build that keeps PacBio reads with 5mC+5hmC > 1
  
  ljwharbers
  and
  claude
  committed
  4d71114
- docs: changelog entry for the patched modkit container (#188)
  
  ljwharbers
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  claude
  committed
  03922de
Commits on Sep 3, 2026
- feat(modkit): add modkit_args (default --cpg --modified-bases 5mC) and modkit_phased options
  
  ljwharbers
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  claude
  committed
  242366d
- docs: document modkit_args and modkit_phased (#188)
  
  ljwharbers
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  claude
  committed
  84f7330
- style: trim modkit container and MODULE banner comments
  
  ljwharbers
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  claude
  committed
  b82fd09
Commits on Sep 4, 2026
- docs: note PacBio limitation of --modkit_phased and the 5mC filter (#188)
  
  ljwharbers
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  claude
  committed
  bf271ae
- style: prettier reflow of docs/usage.md
  
  ljwharbers
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  claude
  committed
  3bdb545
- modkit: bump patched container to 6e0afa2 (phased and 5mC-only output on PacBio)
  
  ljwharbers
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  claude
  committed
  0fccbfe
- modkit: pull the patched image as a native SIF under singularity/apptainer
  
  ljwharbers
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  claude
  committed
  a43f844
Commits on Sep 8, 2026
- Merge origin/dev into fix/modkit-pacbio-container
  
  ljwharbers
  and
  claude
  committed
  538bb4b
Commits on Sep 9, 2026
- Merge origin/dev into fix/modkit-pacbio-container
  
  ljwharbers
  and
  claude
  committed
  13a93cd
Commits on Sep 14, 2026