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strelka_and_post_processing.cwl
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strelka_and_post_processing.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
- class: StepInputExpressionRequirement
inputs:
tumor_bam:
type: File
secondaryFiles: [.bai,^.bai]
normal_bam:
type: File
secondaryFiles: [.bai,^.bai]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
interval_list:
type: File
exome_mode:
type: boolean
cpu_reserved:
type: int?
default: 8
normal_sample_name:
type: string
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:
strelka:
run: ../tools/strelka.cwl
in:
tumor_bam: tumor_bam
normal_bam: normal_bam
reference: reference
exome_mode: exome_mode
cpu_reserved: cpu_reserved
out:
[indels, snvs]
process:
scatter: vcf
run: strelka_process_vcf.cwl
in:
vcf: [strelka/snvs, strelka/indels]
out:
[processed_vcf]
merge:
run: ../tools/merge_vcf.cwl
in:
vcfs: process/processed_vcf
out:
[merged_vcf]
rename_tumor_sample:
run: ../tools/replace_vcf_sample_name.cwl
in:
input_vcf: merge/merged_vcf
sample_to_replace:
default: 'TUMOR'
new_sample_name: tumor_sample_name
out:
[renamed_vcf]
rename_normal_sample:
run: ../tools/replace_vcf_sample_name.cwl
in:
input_vcf: rename_tumor_sample/renamed_vcf
sample_to_replace:
default: 'NORMAL'
new_sample_name: normal_sample_name
out:
[renamed_vcf]
index_full:
run: ../tools/index_vcf.cwl
in:
vcf: rename_normal_sample/renamed_vcf
out:
[indexed_vcf]
region_filter:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: index_full/indexed_vcf
interval_list: interval_list
out:
[filtered_vcf]
filter:
run: fp_filter.cwl
in:
reference: reference
bam: tumor_bam
vcf: region_filter/filtered_vcf
variant_caller:
valueFrom: "strelka"
sample_name: tumor_sample_name
out:
[unfiltered_vcf, filtered_vcf]