X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/aa289173560cd4466d890f3a63927650e37d8aa7..cec9a7f6a83fc2596e042e8adc6179b202f92a6e:/cwl/helper/getfastq.cwl

diff --git a/cwl/helper/getfastq.cwl b/cwl/helper/getfastq.cwl
deleted file mode 100644
index a38bc91..0000000
--- a/cwl/helper/getfastq.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-$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};
-  }