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Merged
Opened Jan 08, 2020 by van den Berg@rrvandenbergOwner

Deprecate conda, make pipeline more general

  • Overview 0
  • Commits 19
  • Pipelines 9
  • Changes 26
  1. Deprecate conda in favour of singularity
  2. Convert all test cases to use conda
  3. Fix a bug in the coverage calculation that was caused by singularity
  4. Remove the external gatk.jar file as a dependency
  5. Specify 1 or more vcf files for base recalibration, instead of ONETHOUSAND, HAPMAP, ONETHOUSAND
Edited Jan 10, 2020 by van den Berg
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Reference: klinische-genetica/capture-lumc/hutspot!13
Source branch: known-snps

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