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 e2aaa887eb27a4efe8239dcd52434673e39b7365..59c677112791346313f16a73c932fa66c8b6b8e5 100644 (file)
--- a/WGS-processing/cwl/helper/getfastq.cwl
+++ b/WGS-processing/cwl/helper/getfastq.cwl
@@ -1,6 +1,6 @@
 class: ExpressionTool
 cwlVersion: v1.1
-label: Find matching FASTQ pairs 
+label: Find matching FASTQ pairs
 requirements:
   InlineJavascriptRequirement: {}
 
@@ -8,7 +8,7 @@ inputs:
   fastqdir:
     type: Directory
     label: Input directory of FASTQs
-    loadListing: 'shallow_listing' 
+    loadListing: 'shallow_listing'
 
 outputs:
   fastq1: 
@@ -41,6 +41,7 @@ expression: |
     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);
       }
@@ -74,6 +75,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl