forked from genome/analysis-workflows
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workflow.cwl
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workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "strelka workflow"
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
tumor_bam:
type: File
secondaryFiles: [^.bai]
normal_bam:
type: File
secondaryFiles: [^.bai]
reference:
type: File
secondaryFiles: [.fai]
interval_list:
type: File
exome_mode:
type: boolean
outputs:
merged_vcf:
type: File
outputSource: index_filtered/indexed_vcf
secondaryFiles: [.tbi]
steps:
strelka:
run: strelka.cwl
in:
tumor_bam: tumor_bam
normal_bam: normal_bam
reference: reference
exome_mode: exome_mode
out:
[indels, snvs]
process:
scatter: vcf
run: process_vcf.cwl
in:
vcf: [strelka/snvs, strelka/indels]
out:
[processed_vcf]
merge:
run: ../detect_variants/merge.cwl
in:
vcfs: [process/processed_vcf]
out:
[merged_vcf]
index_full:
run: ../detect_variants/index.cwl
in:
vcf: merge/merged_vcf
out:
[indexed_vcf]
region_filter:
run: ../detect_variants/select_variants.cwl
in:
reference: reference
vcf: index_full/indexed_vcf
interval_list: interval_list
out:
[filtered_vcf]
index_filtered:
run: ../detect_variants/index.cwl
in:
vcf: region_filter/filtered_vcf
out:
[indexed_vcf]