Workflow: Detect DoCM variants

Fetched 2023-01-05 07:51:36 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs bam bam gatk_haplotypecaller HaplotypeCaller (GATK4) bam->gatk_haplotypecaller bam reference reference reference->gatk_haplotypecaller reference docm_vcf docm_vcf docm_vcf->gatk_haplotypecaller docm_vcf interval_list interval_list interval_list->gatk_haplotypecaller interval_list unfiltered_vcf unfiltered_vcf filtered_vcf filtered_vcf bgzip bgzip VCF index vcf index bgzip->index vcf docm_filter docm filter docm_filter->bgzip file index->filtered_vcf gatk_haplotypecaller->unfiltered_vcf gatk_haplotypecaller->docm_filter docm_out
Workflow as SVG
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  • 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/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/subworkflows/docm_germline.cwl