/
gatk_haplotypecaller_iterator.cwl
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/
gatk_haplotypecaller_iterator.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "scatter GATK HaplotypeCaller over intervals"
requirements:
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
bam:
type: File
secondaryFiles: [^.bai]
emit_reference_confidence:
type:
type: enum
symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
dbsnp_vcf:
type: File?
secondaryFiles: [.tbi]
contamination_fraction:
type: string?
max_alternate_alleles:
type: int?
ploidy:
type: int?
read_filter:
type: string?
output_prefix:
type: string?
doc: 'an optional string to prepend to the output filename'
outputs:
gvcf:
type: File[]
outputSource: haplotype_caller/gvcf
secondaryFiles: [.tbi]
steps:
haplotype_caller:
scatter: [intervals]
run: ../tools/gatk_haplotype_caller.cwl
in:
reference: reference
bam: bam
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
dbsnp_vcf: dbsnp_vcf
contamination_fraction: contamination_fraction
max_alternate_alleles: max_alternate_alleles
ploidy: ploidy
read_filter: read_filter
output_file_name:
source: output_prefix
valueFrom: '${
var prefix = self !== null ? self : "";
if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) {
return prefix + inputs.intervals[0] + ".g.vcf.gz";
} else {
return prefix + "output.g.vcf.gz";
}
}'
out:
[gvcf]