/
gatk-4.0.0.0-library-cram-to-gvcfs.cwl
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gatk-4.0.0.0-library-cram-to-gvcfs.cwl
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$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
hints:
ResourceRequirement:
ramMin: 4000
coresMin: 1
tmpdirMin: 1000
arv:RuntimeConstraints:
keep_cache: 1024
outputDirType: keep_output_dir
cwltool:LoadListingRequirement:
loadListing: no_listing
arv:IntermediateOutput:
outputTTL: 2592000
inputs:
- id: library_cram
type: File
- id: chunks
type: int
- id: intersect_file
type: File
- id: ref_fasta_files
type: File[]
- id: haploid_chromosome_regex
type: string
default: "^(chr)?Y$"
- id: pcr_free
type: boolean
default: true
steps:
- id: cram_get_fasta
run: cram-get-fasta.cwl
in:
input_cram: library_cram
ref_fasta_files: ref_fasta_files
out:
- reference_fasta
- reference_dict
- id: cap_crams
run: capmq.cwl
in:
library_cram: library_cram
reference_fasta: cram_get_fasta/reference_fasta
out:
- capped_file
- id: haplotype_caller_diploid
run: gatk-4.0.0.0-haplotypecaller.cwl
in:
library_cram: cap_crams/capped_file
chunks: chunks
intersect_file: intersect_file
reference_fasta: cram_get_fasta/reference_fasta
reference_dict: cram_get_fasta/reference_dict
ploidy:
default: 2
pcr_free: pcr_free
out:
- gvcf_files
- intervals
- id: haplotype_caller_haploid
run: gatk-4.0.0.0-haplotypecaller.cwl
in:
library_cram: cap_crams/capped_file
chunks:
default: 1
intersect_file: intersect_file
reference_fasta: cram_get_fasta/reference_fasta
reference_dict: cram_get_fasta/reference_dict
ploidy:
default: 1
include_chromosome_regex: haploid_chromosome_regex
pcr_free: pcr_free
out:
- gvcf_files
- intervals
outputs:
- id: gvcf_files_diploid
type: File[]
linkMerge: merge_flattened
outputSource:
- haplotype_caller_diploid/gvcf_files
- id: intervals_diploid
type: File[]
linkMerge: merge_flattened
outputSource:
- haplotype_caller_diploid/intervals
- id: gvcf_files_haploid
type: File[]
linkMerge: merge_flattened
outputSource:
- haplotype_caller_haploid/gvcf_files
- id: intervals_haploid
type: File[]
linkMerge: merge_flattened
outputSource:
- haplotype_caller_haploid/intervals
- id: reference
type: File
outputSource: cram_get_fasta/reference_fasta