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
43 baseCommand: /gatk/gatk
51 ${function compare(a, b) {
52 var baseA = a.basename;
53 var baseB = b.basename;
58 } else if (baseA < baseB) {
65 sortedarray = inputs.gvcfarray.sort(compare)
68 for (var i = 0; i < sortedarray.length; i++) {
69 var name = sortedarray[i];
70 if (name.nameext ==='.gz' ) {
71 samples.push(name.path);
77 for (var i = 0; i < samples.length; i++) {
79 sampleinput = sampleinput + "-I " + s1 + " "
85 valueFrom: $(inputs.sample).g.vcf.gz