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KFDRC Unified Alignment Production Workflow
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@dmiller15 dmiller15 released this 03 Jun 14:45
· 169 commits to master since this release
v2.0.0
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Learn about vigilant mode.

The primary highlight of this release is a new workflow named kfdrc_alignment_wf_cyoa.cwl. This workflow replaces all existing workflows, which have been moved to the workflows-deprecated folder.

Key features of this new workflow:

  • Accepts SE FASTQs, PE FASTQs, and BAMs (or any combination of these) as inputs
  • Minimally converts the input into a CRAM with the option to create a gVCF
  • Breaks up CollectMultipleMetrics step into individual metrics steps
  • See the README and workflow doc for more...

Additional fixes:

  • Tab characters in python_createsequencegroups.cwl tool have been replaced with their ASCII code equivalent (allows tool to be run using cwltool)
  • Bug fix for sambamba_merge_anylist.cwl tool where it would fail with only one BAM input. The tool now correctly passes the BAM when only one is input
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