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Updating cwl and yml for intervals and other changes
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
getfastq.cwl
diff --git
a/WGS-processing/cwl/helper/getfastq.cwl
b/WGS-processing/cwl/helper/getfastq.cwl
index 035b4c3135695d3c1607e5d39b4e1f41fb8c6bc6..59c677112791346313f16a73c932fa66c8b6b8e5 100644
(file)
--- a/
WGS-processing/cwl/helper/getfastq.cwl
+++ b/
WGS-processing/cwl/helper/getfastq.cwl
@@
-41,6
+41,7
@@
expression: |
var fastq2 = [];
for (var i = 0; i < inputs.fastqdir.listing.length; i++) {
var name = inputs.fastqdir.listing[i];
var fastq2 = [];
for (var i = 0; i < inputs.fastqdir.listing.length; i++) {
var name = inputs.fastqdir.listing[i];
+ name.format = 'http://edamontology.org/format_1930'
if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
fastq1.push(name);
}
if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
fastq1.push(name);
}