3 label: Gathering vcf using Picard
5 arv: "http://arvados.org/cwl#"
6 cwltool: "http://commonwl.org/cwltool#"
10 dockerPull: broadinstitute/gatk:4.1.7.0
11 ShellCommandRequirement: {}
12 InlineJavascriptRequirement: {}
18 arv:RuntimeConstraints:
19 outputDirType: keep_output_dir
24 label: Input directory of gvcfs
25 loadListing: 'shallow_listing'
45 baseCommand: /gatk/gatk
53 ${function compare(a, b) {
54 var baseA = a.basename;
55 var baseB = b.basename;
60 } else if (baseA < baseB) {
67 for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
68 var name = inputs.gvcfdir.listing[i];
69 if (name.nameext ==='.gz' ) {
70 samples.push(name.path);
73 samples = samples.sort(compare);
76 for (var i = 0; i < samples.length; i++) {
78 sampleinput = sampleinput + "-I " + s1 + " "
84 valueFrom: $(inputs.sample).g.vcf.gz