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Check and update config defaults #528

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ericblanc20 opened this issue Jul 5, 2024 · 0 comments · May be fixed by #532
Open
8 tasks

Check and update config defaults #528

ericblanc20 opened this issue Jul 5, 2024 · 0 comments · May be fixed by #532

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@ericblanc20
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ericblanc20 commented Jul 5, 2024 •
edited by tedil
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The main configuration template & the step defaults should be checked for consistency and updated to reflect the new filesystems.

  • main configuration: new locations for GRCh37/hs37d5 genome release & friends
  • main configuration: add similar defaults for GRCh38 in comments (GRCh38.d1.vd1 used in somatic branch)
  • main configuration: possibly add another GRCh38 flavor for germline usage
  • main configuration: add feature annotation for expression, neo-epitope prediction, ...
  • ngs_mapping: indices for bwa & bwa_mem2 tools, hs37d5, possibly GRCh38.d1.vd1
  • somatic_variant_calling: default germline variants, panel of normals & common variants (GATK)
  • somatic_variant_annotation: default VEP repositories
  • many steps: exome panels
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docs: Check & update of configuration defaults (first part) bihealth/snappy-pipeline
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