Workflow: Detect DoCM variants

Fetched 2023-01-04 18:59:24 GMT
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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
bam File
docm_vcf File
reference File
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 (GATK4)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a/definitions/subworkflows/docm_germline.cwl