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gatk4_cohort_genotyping.cwl
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gatk4_cohort_genotyping.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
gvcf_files:
type: File[]
secondaryFiles: [.tbi]
reference:
type: File
secondaryFiles: [.fai, ^.dict]
bed_file: File
thread_count: int
number_of_chunks: int
output_prefix: string
cromwell_engine: boolean
outputs:
time_metrics_from_gatk4_cohort_genotyping:
type: File
outputSource: genomel_pdc_gatk4_cohort_genotyping/time_metrics
time_metrics_from_picard_sortvcf:
type: File
outputSource: picard_sortvcf/time_metrics
time_metrics_from_selectvariants:
type: File
outputSource: gatk3_selectvariants/time_metrics
gatk4_cohort_genotyping_vcf:
type: File
outputSource: gatk3_selectvariants/output_vcf
steps:
genomel_pdc_gatk4_cohort_genotyping:
run: ../../tools/variant_calling/genomel_gatk4_cohort_genotyping.cwl
in:
job_uuid: job_uuid
gvcf_files: gvcf_files
reference: reference
bed_file: bed_file
thread_count: thread_count
number_of_chunks: number_of_chunks
cromwell_engine: cromwell_engine
out: [vcf_list, time_metrics]
picard_sortvcf:
run: ../../tools/variant_calling/picard_sortvcf.cwl
in:
job_uuid: job_uuid
vcf: genomel_pdc_gatk4_cohort_genotyping/vcf_list
reference_dict:
source: reference
valueFrom: $(self.secondaryFiles[1])
output_prefix:
source: output_prefix
valueFrom: $(self + '.srt')
out: [sorted_vcf, time_metrics]
gatk3_selectvariants:
run: ../../tools/variant_calling/gatk3_selectvariants.cwl
in:
job_uuid: job_uuid
input_vcf: picard_sortvcf/sorted_vcf
reference: reference
output_prefix:
source: [job_uuid, output_prefix]
valueFrom: $(self[0] + '.' + self[1] + '.gatk4')
out: [output_vcf, time_metrics]