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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: "Varscan Workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
reference:
type: File
secondaryFiles: [.fai]
tumor_bam:
type: File
normal_bam:
type: File
interval_list:
type: File
outputs:
snvs:
type: File
outputSource: index_snvs/indexed_vcf
secondaryFiles: [.tbi]
indels:
type: File
outputSource: index_indels/indexed_vcf
secondaryFiles: [.tbi]
merged_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [.tbi]
steps:
intervals_to_bed:
run: intervals_to_bed.cwl
in:
interval_list: interval_list
out:
[interval_bed]
varscan:
run: varscan.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
roi_bed: intervals_to_bed/interval_bed
out:
[somatic_snvs, somatic_indels, somatic_hc_snvs, somatic_hc_indels]
bgzip_and_index_snvs:
run: bgzip_and_index.cwl
in:
vcf: varscan/somatic_snvs
out:
[indexed_vcf]
bgzip_and_index_hc_snvs:
run: bgzip_and_index.cwl
in:
vcf: varscan/somatic_hc_snvs
out:
[indexed_vcf]
bgzip_and_index_indels:
run: bgzip_and_index.cwl
in:
vcf: varscan/somatic_indels
out:
[indexed_vcf]
bgzip_and_index_hc_indels:
run: bgzip_and_index.cwl
in:
vcf: varscan/somatic_hc_indels
out:
[indexed_vcf]
merge_snvs:
run: set_filter_status.cwl
in:
vcf: bgzip_and_index_snvs/indexed_vcf
filtered_vcf: bgzip_and_index_hc_snvs/indexed_vcf
reference: reference
out:
[merged_vcf]
index_snvs:
run: ../detect_variants/index.cwl
in:
vcf: merge_snvs/merged_vcf
out:
[indexed_vcf]
merge_indels:
run: set_filter_status.cwl
in:
vcf: bgzip_and_index_indels/indexed_vcf
filtered_vcf: bgzip_and_index_hc_indels/indexed_vcf
reference: reference
out:
[merged_vcf]
index_indels:
run: ../detect_variants/index.cwl
in:
vcf: merge_indels/merged_vcf
out:
[indexed_vcf]
merge:
run: ../detect_variants/merge.cwl
in:
vcfs: [index_snvs/indexed_vcf, index_indels/indexed_vcf]
out:
[merged_vcf]
index:
run: ../detect_variants/index.cwl
in:
vcf: merge/merged_vcf
out:
[indexed_vcf]