updating preprocessing code

[arvados-tutorial.git] / src / preprocessing / cwl / getfiles.cwl

diff --git a/src/preprocessing/cwl/getfiles.cwl b/src/preprocessing/cwl/getfiles.cwl
new file mode 100644 (file)
index 0000000..3d8d3fd
--- /dev/null
+++ b/src/preprocessing/cwl/getfiles.cwl
@@ -0,0 +1,40 @@
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+class: ExpressionTool
+label: Create list of bams from directory
+cwlVersion: v1.1
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  bamdir:
+    type: Directory
+    label: Directory of input bams
+    loadListing: shallow_listing
+ 
+outputs:
+  tarzipbams:
+    type: File[]
+    label: Array of bams 
+  samplenames:
+    type: string[]
+    label: Array of sample names
+
+expression: |
+  ${
+    var tarzipbams = [];
+    var samplenames = [];
+
+    for (var i = 0; i < inputs.bamdir.listing.length; i++) {
+      var file = inputs.bamdir.listing[i];
+      if (file.nameext == '.tgz') {
+        var main = file;
+        var sample = file.nameroot;
+        sample = sample.replace(".bam","")
+        tarzipbams.push(main);
+        samplenames.push(sample);
+      }
+    }
+    return {"tarzipbams": tarzipbams, "samplenames": samplenames};
+  }
+