Cwl

workflows/kallisto/workflow.cwl

+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: Workflow
 
@@ -7,62 +8,58 @@ requirements:
   InlineJavascriptRequirement: {}
 
 inputs:
-  IndexInput: File[]
-  InputReadsMultipleSamples:
-    type: 
-      type: array
-      items: 
-        type: array
-        items: File
-  # numCharsFileName:
-  #   type: int
-  #   default: 6
-  numUnderscoresFileName:
-    type: int
-    default: 2
-  isSingle: boolean
-  FragmentLength: double?  
-  StandardDeviation: double?
-  BootstrapSamples: int?
-  resultsFolder: string
+    IndexInput: File[]
+    sampleRecord:
+        type:
+          type: array
+          items:
+            type: record
+            fields:
+              readsOfOneSample:
+                type: File[]
+              sampleName:
+                type: string?
+    isSingle: boolean
+    FragmentLength: double?
+    StandardDeviation: double?
+    BootstrapSamples: int?
+    resultsFolder: string
 
 steps:
-  index:
-    run: kallisto-index.cwl
-    in:
-      InputFiles: IndexInput
-      IndexName: 
-        source: IndexInput
-        valueFrom: $(self[0].nameroot)
-    out: [index]
-  quant:
-    run: kallisto-quant.cwl
-    scatter: 
-      - InputReads
-      - QuantOutfolder
-    scatterMethod: dotproduct
-    in:
-      InputReads: InputReadsMultipleSamples
-      # numChars:
-      #   source: numCharsFileName
-      numUnderscores: numUnderscoresFileName
-      QuantOutfolder:
-        source: InputReadsMultipleSamples
-        # valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
-        valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
-      Index: index/index
-      isSingle: isSingle
-      FragmentLength: FragmentLength 
-      StandardDeviation: StandardDeviation
-      BootstrapSamples: BootstrapSamples
-    out: [outFolder]
-  collectResults:
-    run: ./yield-dirInDestination.cwl
-    scatter: inDir
-    in:
-      inDir: quant/outFolder
-      destinationDir: resultsFolder
-    out: [outDir]
+    index:
+        run: kallisto-index.cwl
+        in:
+            InputFiles: IndexInput
+            IndexName:
+                source: IndexInput
+                valueFrom: $(self[0].nameroot)
+        out: [index]
+
+    quant:
+        run: kallisto-quant.cwl
+        scatter: [InputReads, QuantOutfolder]
+        scatterMethod: dotproduct
+        in:
+            InputReads:
+                source: sampleRecord
+                valueFrom: $(self.readsOfOneSample)
+            QuantOutfolder:
+                source: sampleRecord
+                valueFrom: $(self.sampleName)
+            Index: index/index
+            isSingle: isSingle
+            FragmentLength: FragmentLength
+            StandardDeviation: StandardDeviation
+            BootstrapSamples: BootstrapSamples
+        out: [outFolder]
+
+    collectResults:
+        run: ./yield-dirInDestination.cwl
+        scatter: inDir
+        in:
+            inDir: quant/outFolder
+            destinationDir: resultsFolder
+        out: [outDir]
 
 outputs:
   finalOut: