3 label: Gather GVCF using Picard
6 arv: "http://arvados.org/cwl#"
7 cwltool: "http://commonwl.org/cwltool#"
11 dockerPull: broadinstitute/gatk:4.1.7.0
12 ShellCommandRequirement: {}
13 InlineJavascriptRequirement: {}
19 arv:RuntimeConstraints:
20 outputDirType: keep_output_dir
25 label: Input directory of GVCFs
26 loadListing: 'shallow_listing'
32 format: edam:format_1929 # FASTA
33 label: Reference genome
45 format: edam:format_3016 # GVCF
52 baseCommand: /gatk/gatk
60 ${function compare(a, b) {
61 var baseA = a.basename;
62 var baseB = b.basename;
67 } else if (baseA < baseB) {
74 for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
75 var name = inputs.gvcfdir.listing[i];
76 if (name.nameext ==='.gz' ) {
77 samples.push(name.path);
80 samples = samples.sort(compare);
83 for (var i = 0; i < samples.length; i++) {
85 sampleinput = sampleinput + "-I " + s1 + " "
91 valueFrom: $(inputs.sample).g.vcf.gz
93 s:codeRepository: https://github.com/arvados/arvados-tutorial
94 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
97 s: https://schema.org/
98 edam: http://edamontology.org/
99 arv: "http://arvados.org/cwl#"
100 cwltool: "http://commonwl.org/cwltool#"
103 # - https://schema.org/version/latest/schema.rdf
104 # - http://edamontology.org/EDAM_1.18.owl