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gatk-4.0.0.0-haplotypecaller-genotypegvcfs-libraries.cwl
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gatk-4.0.0.0-haplotypecaller-genotypegvcfs-libraries.cwl
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$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement
hints:
ResourceRequirement:
ramMin: 4000
coresMin: 1
tmpdirMin: 1000
arv:RuntimeConstraints:
keep_cache: 1024
outputDirType: keep_output_dir
cwltool:LoadListingRequirement:
loadListing: no_listing
arv:IntermediateOutput:
outputTTL: 2592000
inputs:
- id: library_crams
type: File[]
- id: chunks
type: int
- id: intersect_file
type: File
- id: ref_fasta_files
type: File[]
- id: output_basename
type: string
default: output
- id: haploid_chromosome_regex
type: string
default: "^(chr)?Y$"
steps:
- id: haplotype_caller
scatter:
- library_cram
run: gatk-4.0.0.0-library-cram-to-gvcfs.cwl
in:
library_cram: library_crams
chunks: chunks
intersect_file: intersect_file
ref_fasta_files: ref_fasta_files
haploid_chromosome_regex: haploid_chromosome_regex
out:
- gvcf_files_diploid
- intervals_diploid
- gvcf_files_haploid
- intervals_haploid
- reference
- id: joint_calling_diploid
run: gatk-4.0.0.0-joint-calling.cwl
in:
gvcf_files: haplotype_caller/gvcf_files_diploid
intervals:
source: haplotype_caller/intervals_diploid
valueFrom: $(self[0])
reference:
source: haplotype_caller/reference
valueFrom: $(self[0])
output_filename:
source: output_basename
valueFrom: $(self).diploid.vcf.gz
out:
- out
- id: joint_calling_haploid
run: gatk-4.0.0.0-joint-calling.cwl
in:
gvcf_files: haplotype_caller/gvcf_files_haploid
intervals:
source: haplotype_caller/intervals_haploid
valueFrom: $(self[0])
reference:
source: haplotype_caller/reference
valueFrom: $(self[0])
output_filename:
source: output_basename
valueFrom: $(self).haploid.vcf.gz
out:
- out
outputs:
- id: output_diploid
type: File
outputSource: joint_calling_diploid/out
- id: output_haploid
type: File
outputSource: joint_calling_haploid/out