Workflow: Detect DoCM variants

Fetched 2023-01-04 21:00:41 GMT
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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
cram File
docm_vcf File
reference String
interval_list File

Steps

ID Runs Label Doc
bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
docm_filter
../tools/single_sample_docm_filter.cwl (CommandLineTool)
docm filter
gatk_haplotypecaller
../tools/docm_gatk_haplotype_caller.cwl (CommandLineTool)
HaplotypeCaller (GATK 3.6)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/891c996dbd23d8154ec7609a56da3de841ae124c/definitions/subworkflows/docm_germline.cwl