/
mutect.cwl
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/
mutect.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "mutect parallel workflow"
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: [^.bai, .bai]
normal_bam:
type: File?
secondaryFiles: [^.bai]
interval_list:
type: File
scatter_count:
type: int
tumor_sample_name:
type: string
outputs:
unfiltered_vcf:
type: File
outputSource: filter/unfiltered_vcf
secondaryFiles: [.tbi]
filtered_vcf:
type: File
outputSource: filter/filtered_vcf
secondaryFiles: [.tbi]
steps:
split_interval_list:
run: ../tools/split_interval_list.cwl
in:
interval_list: interval_list
scatter_count: scatter_count
out: [split_interval_lists]
mutect:
scatter: interval_list
run: ../tools/mutect.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
interval_list: split_interval_list/split_interval_lists
out:
[vcf]
merge:
run: ../tools/merge_vcf.cwl
in:
vcfs: mutect/vcf
out:
[merged_vcf]
index:
run: ../tools/index_vcf.cwl
in:
vcf: merge/merged_vcf
out:
[indexed_vcf]
filter:
run: fp_filter.cwl
in:
reference: reference
bam: tumor_bam
vcf: index/indexed_vcf
variant_caller:
valueFrom: "mutect"
sample_name: tumor_sample_name
out:
[unfiltered_vcf, filtered_vcf]