Arc cwl

workflows/kallisto/workflow.cwl

@@ -8,56 +8,56 @@ requirements:
   InlineJavascriptRequirement: {}
 
 inputs:
-    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
+  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]
+  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: [kallistoQuantOutDir]
-    collectResults:
-        run: ./gather-dirs.cwl
-        in:
-            inDirs: quant/kallistoQuantOutDir
-            destinationDir: resultsFolder
-        out: [outDir]
+  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: [kallistoQuantOutDir]
+  collectResults:
+    run: ./gather-dirs.cwl
+    in:
+      inDirs: quant/kallistoQuantOutDir
+      destinationDir: resultsFolder
+    out: [outDir]
 
 outputs:
   kallistoOutDir: