Cwl

workflows/kallisto/workflow.cwl

@@ -8,20 +8,18 @@ requirements:
 
 inputs:
   IndexInput: File[]
-  InputReadsMultipleSamples:
-    type: 
+  sampleRecord:
+    type:
       type: array
-      items: 
-        type: array
-        items: File
-  # numCharsFileName:
-  #   type: int
-  #   default: 6
-  numUnderscoresFileName:
-    type: int
-    default: 2
+      items:
+        type: record
+        fields:
+          readsOfOneSample:
+            type: File[]
+          sampleName:
+            type: string?
   isSingle: boolean
-  FragmentLength: double?  
+  FragmentLength: double?
   StandardDeviation: double?
   BootstrapSamples: int?
   resultsFolder: string
@@ -31,28 +29,24 @@ steps:
     run: kallisto-index.cwl
     in:
       InputFiles: IndexInput
-      IndexName: 
+      IndexName:
         source: IndexInput
         valueFrom: $(self[0].nameroot)
     out: [index]
   quant:
     run: kallisto-quant.cwl
-    scatter: 
-      - InputReads
-      - QuantOutfolder
+    scatter: [InputReads, QuantOutfolder]
     scatterMethod: dotproduct
     in:
-      InputReads: InputReadsMultipleSamples
-      # numChars:
-      #   source: numCharsFileName
-      numUnderscores: numUnderscoresFileName
+      InputReads:
+        source: sampleRecord
+        valueFrom: $(self.readsOfOneSample)
       QuantOutfolder:
-        source: InputReadsMultipleSamples
-        # valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
-        valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
+        source: sampleRecord
+        valueFrom: $(self.sampleName)
       Index: index/index
       isSingle: isSingle
-      FragmentLength: FragmentLength 
+      FragmentLength: FragmentLength
       StandardDeviation: StandardDeviation
       BootstrapSamples: BootstrapSamples
     out: [outFolder]