/
germline_workflow.cwl
54 lines (53 loc) · 1.25 KB
/
germline_workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Detect DoCM variants"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: string
cram:
type: File
secondaryFiles: [^.crai]
docm_vcf:
type: File
secondaryFiles: [.tbi]
interval_list:
type: File
outputs:
unfiltered_vcf:
type: File
outputSource: gatk_haplotypecaller/docm_out
filtered_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [.tbi]
steps:
gatk_haplotypecaller:
run: germline_gatk_haplotypecaller.cwl
in:
reference: reference
cram: cram
docm_vcf: docm_vcf
interval_list: interval_list
out:
[docm_out]
docm_filter:
run: single_sample_docm_filter.cwl
in:
docm_out: gatk_haplotypecaller/docm_out
out:
[docm_filter_out]
bgzip:
run: ../detect_variants/bgzip.cwl
in:
file: docm_filter/docm_filter_out
out:
[bgzipped_file]
index:
run: ../detect_variants/index_vcf.cwl
in:
vcf: bgzip/bgzipped_file
out:
[indexed_vcf]