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feat: aligners & variant callers#282

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adthrasher wants to merge 154 commits into
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feat/minimap2
Open

feat: aligners & variant callers#282
adthrasher wants to merge 154 commits into
mainfrom
feat/minimap2

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@adthrasher
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@adthrasher adthrasher commented Dec 3, 2025

Adds new WDL task implementations:

  • bwa-mem2
  • minimap2
  • hisat2
  • vg giraffe
  • DeepVariant / DeepSomatic
  • Strelka
  • Manta
  • Clair3
  • NGSEP

I also created a new evaluation directory under workflows (maybe it should be placed somewhere else) that has workflows for running a sample through multiple analyses in parallel for comparison purposes.

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@adthrasher adthrasher marked this pull request as draft December 9, 2025 16:12
@adthrasher adthrasher self-assigned this Dec 9, 2025
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
@adthrasher adthrasher requested a review from a-frantz May 13, 2026 17:02
@adthrasher adthrasher marked this pull request as ready for review May 13, 2026 17:02
@adthrasher
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Lint failures are for EmptyOutputs, which is addressed in #315

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