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somatic_exome cram version #973

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This PR is a starting point for the migration of our workflows to use crams from beginning to end. Aside from variable name changes, this PR includes the minimum necessary changes needed to make the somatic_exome workflow use crams; this has been verified with the HCC1395 subset example data, but no further testing has been completed so far.

Several tools are unable to directly work with cram files, and require bam to cram conversion steps in the new version of the pipeline included in this PR:

  • fp_filter.cwl: This is a perl script, forked from an upstream repo; this was initially assumed to not support bams due to unfamiliarity with the script, but upon closer inspection, it appears that the input bam file is not used aside from passing it to bam-readcount. With the latest cram supporting version of bam readcount, patching fp_filter to accept bam files should be doable.
  • pindel.cwl: pindel does not support cram files, and the official repository has been archived
  • verify_bam_id.cwl: the verify_bam_id tool does not support cram files, and an issue in the official repo suggests another tool

Several new tools are introduced:

  • name_sort_samtools.cwl: sambamba does not support cram files
  • merge_crams.cwl: this repo did not yet have a tool for merging cram files

Finally, several tools use docker images that are currently unofficial:

@etal
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etal commented Dec 8, 2020

Hey John, thanks for the patches to CNVkit! I've merged them in that repo, and I'll see about rolling another release and Docker image so that you can use the upstream directly.

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