7 dockerPull: broadinstitute/gatk:4.1.7.0
8 ShellCommandRequirement: {}
9 InlineJavascriptRequirement: {}
15 arv:RuntimeConstraints:
16 outputDirType: keep_output_dir
21 format: edam:format_3016 # GVCF
22 label: GVCFs for given intervals
28 format: edam:format_1929 # FASTA
29 label: Reference genome
41 format: edam:format_3016 # GVCF
48 baseCommand: /gatk/gatk
56 ${function compare(a, b) {
57 var baseA = a.basename;
58 var baseB = b.basename;
63 } else if (baseA < baseB) {
70 sortedarray = inputs.gvcfarray.sort(compare)
73 for (var i = 0; i < sortedarray.length; i++) {
74 var name = sortedarray[i];
75 if (name.nameext ==='.gz' ) {
76 samples.push(name.path);
82 for (var i = 0; i < samples.length; i++) {
84 sampleinput = sampleinput + "-I " + s1 + " "
90 valueFrom: $(inputs.sample).g.vcf.gz
92 s:codeRepository: https://github.com/arvados/arvados-tutorial
93 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
96 s: https://schema.org/
97 edam: http://edamontology.org/
98 arv: "http://arvados.org/cwl#"
99 cwltool: "http://commonwl.org/cwltool#"
102 # - https://schema.org/version/latest/schema.rdf
103 # - http://edamontology.org/EDAM_1.18.owl