/
germline_workflow.cwl
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/
germline_workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Varscan Workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type: string
cram:
type: File
secondaryFiles: [^.crai]
interval_list:
type: File
strand_filter:
type: int?
default: 0
min_coverage:
type: int?
default: 8
min_var_freq:
type: float?
default: 0.1
min_reads:
type: int?
default: 2
p_value:
type: float?
default: 0.99
max_normal_freq:
type: float?
sample_name:
type: string
outputs:
unfiltered_vcf:
type: File
outputSource: filter/unfiltered_vcf
filtered_vcf:
type: File
outputSource: filter/filtered_vcf
secondaryFiles: [.tbi]
steps:
intervals_to_bed:
run: intervals_to_bed.cwl
in:
interval_list: interval_list
out:
[interval_bed]
varscan:
run: varscan_germline.cwl
in:
reference: reference
cram: cram
roi_bed: intervals_to_bed/interval_bed
strand_filter: strand_filter
min_coverage: min_coverage
min_var_freq: min_var_freq
min_reads: min_reads
p_value: p_value
sample_name: sample_name
out:
[variants]
bgzip_and_index:
run: bgzip_and_index.cwl
in:
vcf: varscan/variants
out:
[indexed_vcf]
filter:
run: ../fp_filter/workflow.cwl
in:
reference: reference
cram: cram
vcf: bgzip_and_index/indexed_vcf
variant_caller:
valueFrom: "varscan"
sample_name: sample_name
min_var_freq: min_var_freq
out:
[unfiltered_vcf, filtered_vcf]