/
haplotypecaller.cwl
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/
haplotypecaller.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
job_uuid: string
bam_file:
type: File
secondaryFiles: [^.bai]
reference:
type: File
secondaryFiles: [.fai, ^.dict]
interval: File
snp_ref:
type: File
secondaryFiles: [.tbi]
sample_name: string?
outputs:
time_metrics_from_gatk3_haplotypecaller:
type: File
outputSource: gatk3_haplotypecaller/time_metrics
time_metrics_from_picard_sortvcf:
type: File
outputSource: picard_sortvcf/time_metrics
haplotypecaller_sorted_vcf:
type: File
outputSource: picard_sortvcf/sorted_vcf
steps:
gatk3_haplotypecaller:
run: ../../tools/variant_calling/gatk3_haplotypercaller.cwl
in:
job_uuid: job_uuid
bam_file: bam_file
reference: reference
interval: interval
snp_ref: snp_ref
sample_name: sample_name
out: [gvcf_list, time_metrics]
picard_sortvcf:
run: ../../tools/variant_calling/picard_sortvcf.cwl
in:
job_uuid: job_uuid
vcf: gatk3_haplotypecaller/gvcf_list
reference_dict:
source: reference
valueFrom: $(self.secondaryFiles[1])
output_prefix:
valueFrom: 'haplotypecaller.g'
out: [sorted_vcf, time_metrics]