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#"
hints:
ResourceRequirement:
ramMin: 20000
- coresMin: 4
+ coresMin: 4
arv:RuntimeConstraints:
outputDirType: keep_output_dir
inputs:
- gvcfdir:
+ 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:
arguments:
- "--java-options"
- - "-Xmx8G"
+ - "-Xmx8G"
- MergeVcfs
- shellQuote: false
- valueFrom: |
+ valueFrom: |
${function compare(a, b) {
var baseA = a.basename;
var baseB = b.basename;
comparison = -1;
}
return comparison;
- }
+ }
var samples = [];
for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
}
- 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