cwlVersion: v1.1
class: CommandLineTool
-label: Gathering vcf using Picard
+label: Gather GVCF using Picard
+
$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
inputs:
gvcfdir:
type: Directory
- label: Input directory of gvcfs
+ label: Input directory of GVCFs
loadListing: 'shallow_listing'
- sample: string
+ sample:
+ type: string
+ label: Sample Name
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
outputs:
gatheredgvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: Gathered GVCF
secondaryFiles:
- .tbi
outputBinding:
}
- prefix: "-O"
valueFrom: $(inputs.sample).g.vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: GVCF generated from GATK Haplotype Caller
+ label: Gathered GVCF
secondaryFiles:
- .tbi
- outputSource: merge-GVCFs/gatheredgvcf
+ outputSource: gather-GVCFs/gatheredgvcf
steps:
splitintervals:
intervallist: splitintervals/intervalfiles
out: [gvcf]
- merge-GVCFs:
+ gather-GVCFs:
run: gather-array-vcf.cwl
in:
gvcfarray: recal-haplotypecaller/gvcf