+++ /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};
- }