forked from genome/analysis-workflows
/
docm_germline.cwl
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docm_germline.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
- File
secondaryFiles: [.fai, ^.dict]
bam:
type: File
secondaryFiles: [^.bai]
docm_vcf:
type: File
secondaryFiles: [.tbi]
interval_list:
type: File
outputs:
unfiltered_vcf:
type: File
outputSource: gatk_haplotypecaller/docm_raw_variants
filtered_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [.tbi]
steps:
gatk_haplotypecaller:
run: ../tools/docm_gatk_haplotype_caller.cwl
in:
reference: reference
bam: bam
docm_vcf: docm_vcf
interval_list: interval_list
out:
[docm_raw_variants]
docm_filter:
run: ../tools/single_sample_docm_filter.cwl
in:
docm_out: gatk_haplotypecaller/docm_raw_variants
out:
[docm_filter_out]
bgzip:
run: ../tools/bgzip.cwl
in:
file: docm_filter/docm_filter_out
out:
[bgzipped_file]
index:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip/bgzipped_file
out:
[indexed_vcf]