Github.com/mwalker174/clarum-utils/reheader_platform

Automatic Tools and Workflows
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clarum-utils

Utility workflows and scripts for CLARUM retro-WGS processing on Terra.

Workflows

reheader_platform.wdl

Fixes an invalid read-group PL (platform) tag in a CRAM. Picard
ValidateSamFile rejects PL:NovaSeq X because PL must use the SAM-spec
controlled vocabulary (ILLUMINA, PACBIO, ONT, …); NovaSeq X is an
instrument model and belongs in PM. The workflow rewrites every @RG:

  • PL:NovaSeq X → PL:ILLUMINA
  • adds PM:NovaSeq X when no PM tag is pr
This is a companion discussion topic for the original entry at github.com/mwalker174/clarum-utils/reheader_platform