/
panel_of_normals.cwl
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/
panel_of_normals.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "mutect panel-of-normals workflow"
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: string
normal_bams:
type: File[]
secondaryFiles: [^.bai]
interval_list:
type: File
scatter_count:
type: int
dbsnp_vcf:
type: File?
secondaryFiles: [.tbi]
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
normal_sample_name:
type: string
outputs:
pon_vcf:
type: File
outputSource: combine/combined_vcf
secondaryFiles: [.tbi]
steps:
mutect:
scatter: tumor_bam
run: ../subworkflows/mutect.cwl
in:
reference: reference
tumor_bam: normal_bams
normal_bam:
default: null
interval_list: interval_list
scatter_count: scatter_count
dbsnp_vcf: dbsnp_vcf
cosmic_vcf: cosmic_vcf
artifact_detection_mode:
default: true
panel_of_normals_vcf:
default: null
tumor_sample_name: normal_sample_name
out:
[unfiltered_vcf]
combine:
run: ../tools/pon_combine_variants.cwl
in:
reference: reference
interval_list: interval_list
normal_vcfs: mutect/unfiltered_vcf
out:
[combined_vcf]