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SV Liftover Code#240

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yashpatel6 wants to merge 26 commits intomainuclahs-cds/metapipeline-DNA:mainfrom yashpatel-sv-liftoveruclahs-cds/metapipeline-DNA:yashpatel-sv-liftoverCopy head branch name to clipboard

+236-108

Commits

Commits on Jan 28, 2025

• Add output saving keys for gSV, sSV, gSNP

  yashpatel6

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  a8e6eff

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• Update call-gSV to always run in workflow

  yashpatel6

  committed
  7f7c9e9

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• Update gSV workflow to identify outputs and handle run when gSV not enabled

  yashpatel6

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  e0fc4af

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• Update gSV runner to output output directory

  yashpatel6

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  e81da93

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• Output sample ID from YAML creation for gSV

  yashpatel6

  committed
  3b11f59

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• Update StableLift to liftover only Delly and not Manta gSV

  yashpatel6

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  72f251c

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• Add output identification workflow for call-gSV

  yashpatel6

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  9b5d823

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Commits on Jan 29, 2025

• Add option to schema

  yashpatel6

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  fe374e3

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• Update pipeline selector with gSV option

  yashpatel6

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  ccf0a7f

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• Update to check for gSV output for liftover

  yashpatel6

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  77bfb9b

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Commits on Jan 30, 2025

• Add output identification info to call-sSV runner

  yashpatel6

  committed
  68e722a

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• Add sSV to schema

  yashpatel6

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  f562735

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• Add sSV to selector and update logic for enabling StableLift

  yashpatel6

  committed
  52e0a8c

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• Add sSV as precursor to StableLift

  yashpatel6

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  eabe899

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• Filter out Manta-sSV

  yashpatel6

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  9469655

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• Fix syntax

  yashpatel6

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  9fa79d1

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• Update YAML creation to output ID

  yashpatel6

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  bafb796

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• Add output identification for call-sSV

  yashpatel6

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  df124e5

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• Update workflow to identify outputs

  yashpatel6

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  8fe2cf9

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• Use .bcf format for DELLY

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Commits on Jan 31, 2025

• Update comment

  yashpatel6

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  ef0b324

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• Fix channel mixing

  yashpatel6

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  6e3ca17

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• Update SV output detection to look for VCFs

  yashpatel6

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  591b279

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• Disable selection of SV liftover

  yashpatel6

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  9261240

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• Update CHANGELOG

  yashpatel6

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  4f13fe4

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• Disable looking for VCF Delly output for now

  yashpatel6

  committed
  3aab0e4

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