Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+label: Converts gvcf to vcf
+
+requirements:
+ - class: DockerRequirement
+ dockerPull: curii/clinvar-report
+ - class: ShellCommandRequirement
+
+hints:
+ ResourceRequirement:
+ ramMin: 10000
+ coresMin: 4
+
+inputs:
+ samplename:
+ type: string
+ gvcf:
+ type: File
+
+outputs:
+ vcf:
+ type: File
+ outputBinding:
+ glob: "*.vcf.gz"
+ secondaryFiles: [.tbi]
+
+arguments:
+ - bcftools
+ - view
+ - prefix: "--min-ac"
+ valueFrom: "1"
+ - $(inputs.gvcf.path)
+ - valueFrom: "-Ov"
+ - prefix: "-o"
+ valueFrom: $(inputs.samplename).vcf
+ - {valueFrom: '&&', shellQuote: false}
+ - bgzip
+ - valueFrom: $(inputs.samplename).vcf
+ - {valueFrom: '&&', shellQuote: false}
+ - tabix
+ - valueFrom: $(inputs.samplename).vcf.gz
class: Workflow
inputs:
- vcf:
+ gvcf:
type: File
+ samplename:
+ type: string
clinvarvcf:
type: File
reportfunc:
outputSource: generate-report/report
steps:
+ gvcf-to-vcf:
+ run: gvcf-to-vcf.cwl
+ in:
+ gvcf: gvcf
+ samplename: samplename
+ out: [vcf]
+
annotate:
run: annotate-vcf.cwl
in:
- vcf: vcf
+ vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]