3 label: Find matching FASTQ pairs
5 InlineJavascriptRequirement: {}
10 label: Input directory of FASTQs
11 loadListing: 'shallow_listing'
16 format: edam:format_1930 # FASTQ
17 label: Half set of pair-end FASTQs (R1)
20 format: edam:format_1930 # FASTQ
21 label: Half set of pair-end FASTQs (R2)
27 ${function compare(a, b) {
28 var baseA = a.basename;
29 var baseB = b.basename;
34 } else if (baseA < baseB) {
42 for (var i = 0; i < inputs.fastqdir.listing.length; i++) {
43 var name = inputs.fastqdir.listing[i];
44 if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
47 if (name.basename.indexOf('_2.fastq.gz') != -1 ) {
52 fastq1 = fastq1.sort(compare)
53 fastq2 = fastq2.sort(compare)
57 for (var i = 0; i < fastq1.length; i++) {
58 var name = fastq1[i].basename;
59 var samplename = name.replace(/_1.fastq.gz/,'');
60 sample.push(samplename);
64 return {"fastq1": fastq1, "fastq2": fastq2, "sample": sample};
68 s:codeRepository: https://github.com/arvados/arvados-tutorial
69 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
72 s: https://schema.org/
73 edam: http://edamontology.org/
74 arv: "http://arvados.org/cwl#"
75 cwltool: "http://commonwl.org/cwltool#"
78 - https://schema.org/version/latest/schema.rdf
79 - http://edamontology.org/EDAM_1.18.owl