--- /dev/null
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+class: ExpressionTool
+cwlVersion: v1.1
+label: Create array of gvcfs to process
+requirements:
+ InlineJavascriptRequirement: {}
+inputs:
+ fastjdir:
+ type: Directory
+ label: Input directory of fastj
+ loadListing: 'shallow_listing'
+outputs:
+ fastq1:
+ type: File[]
+ fastq2:
+ type: File[]
+expression: |
+ ${function compare(a, b) {
+ var baseA = a.basename;
+ var baseB = b.basename;
+
+ var comparison = 0;
+ if (baseA > baseB) {
+ comparison = 1;
+ } else if (baseA < baseB) {
+ comparison = -1;
+ }
+ return comparison;
+ }
+
+ var fastq1 = [];
+ var fastq2 = [];
+ for (var i = 0; i < inputs.fastjdir.listing.length; i++) {
+ var name = inputs.fastjdir.listing[i];
+ if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
+ fastq1.push(name);
+ }
+ if (name.basename.indexOf('_2.fastq.gz') != -1 ) {
+ fastq2.push(name);
+ }
+ }
+
+ fastq1 = fastq1.sort(compare)
+ fastq2 = fastq2.sort(compare)
+
+ return {"fastq1": fastq1, "fastq2": fastq2};
+ }