Updating readme and reorganization

[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 a38bc9125a60652a71c65e7f58d193a47a6663eb..c651771389f2720614f5e33fcab54e325f3a5305 100644 (file)
--- a/WGS-processing/cwl/helper/getfastq.cwl
+++ b/WGS-processing/cwl/helper/getfastq.cwl
@@ -7,15 +7,17 @@ label: Create array of gvcfs to process
 requirements:
   InlineJavascriptRequirement: {}
 inputs:
-  fastjdir:
+  fastqdir:
     type: Directory
-    label: Input directory of fastj
+    label: Input directory of fastqs
     loadListing: 'shallow_listing' 
 outputs:
   fastq1: 
     type: File[]
   fastq2:
     type: File[]
+  sample:
+    type: string[]
 expression: |
   ${function compare(a, b) {
     var baseA = a.basename;
@@ -32,8 +34,8 @@ expression: |
 
     var fastq1 = [];
     var fastq2 = [];
-    for (var i = 0; i < inputs.fastjdir.listing.length; i++) {
-      var name = inputs.fastjdir.listing[i];
+    for (var i = 0; i < inputs.fastqdir.listing.length; i++) {
+      var name = inputs.fastqdir.listing[i];
       if (name.basename.indexOf('_1.fastq.gz') != -1 ) {
         fastq1.push(name);
       }
@@ -44,6 +46,15 @@ expression: |
   
     fastq1 = fastq1.sort(compare)
     fastq2 = fastq2.sort(compare)
+
+    var sample = [];
+
+    for (var i = 0; i < fastq1.length; i++) {
+      var name = fastq1[i].basename;
+      var samplename = name.replace(/_1.fastq.gz/,'');
+      sample.push(samplename);
+      }
+
  
-    return {"fastq1": fastq1, "fastq2": fastq2};
+    return {"fastq1": fastq1, "fastq2": fastq2, "sample": sample};
   }