improve logic to gather output directories from kallisto scatter step

.cwl/cwl-plots/runs/kallisto.svg

@@ -109,15 +109,15 @@
 <path fill="none" stroke="black" d="M79.18,-185.43C89.76,-174.74 104.84,-161.76 121,-155 157.69,-139.66 267.22,-133.56 330.49,-131.27"/>
 <polygon fill="black" stroke="black" points="330.73,-134.77 340.61,-130.93 330.49,-127.77 330.73,-134.77"/>
 </g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
 <g id="node9" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
 <polygon fill="#94ddf4" stroke="black" points="346.06,-38.5 346.06,-74.5 407.94,-74.5 407.94,-38.5 346.06,-38.5"/>
-<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
 </g>
-<!-- kallisto&#45;&gt;finalOut -->
+<!-- kallisto&#45;&gt;kallistoOutDir -->
 <g id="edge8" class="edge">
-<title>kallisto&#45;&gt;finalOut</title>
+<title>kallisto&#45;&gt;kallistoOutDir</title>
 <path fill="none" stroke="black" d="M377,-110.93C377,-103.17 377,-93.78 377,-85.06"/>
 <polygon fill="black" stroke="black" points="380.5,-84.9 377,-74.9 373.5,-84.9 380.5,-84.9"/>
 </g>

.cwl/cwl-plots/workflows/kallisto.svg

@@ -37,15 +37,15 @@
 <path fill="none" stroke="black" d="M491.95,-193.08C456.78,-182.13 394.44,-162.71 348.49,-148.4"/>
 <polygon fill="black" stroke="black" points="349.25,-144.97 338.66,-145.34 347.16,-151.66 349.25,-144.97"/>
 </g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
 <g id="node11" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
 <polygon fill="#94ddf4" stroke="black" points="260.06,-38.5 260.06,-74.5 321.94,-74.5 321.94,-38.5 260.06,-38.5"/>
-<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
 </g>
-<!-- collectResults&#45;&gt;finalOut -->
+<!-- collectResults&#45;&gt;kallistoOutDir -->
 <g id="edge12" class="edge">
-<title>collectResults&#45;&gt;finalOut</title>
+<title>collectResults&#45;&gt;kallistoOutDir</title>
 <path fill="none" stroke="black" d="M291,-111.31C291,-103.29 291,-93.55 291,-84.57"/>
 <polygon fill="black" stroke="black" points="294.5,-84.53 291,-74.53 287.5,-84.53 294.5,-84.53"/>
 </g>

arc.cwl

@@ -50,7 +50,7 @@ steps:
             StandardDeviation:  kallisto_StandardDeviation
             BootstrapSamples:   kallisto_BootstrapSamples
             resultsFolder:      kallisto_resultsFolder
-        out: [finalOut]
+        out: [kallistoOutDir]
 
 
     isaSampleToRawDataSeq:
@@ -65,7 +65,7 @@ steps:
     sleuth:
         run: runs/sleuth/run.cwl
         in:
-            inKallistoResults:      kallisto/finalOut
+            inKallistoResults:      kallisto/kallistoOutDir
             inMetadataFile:         isaSampleToRawDataSeq/output
             inMetadataSample:       sleuth_inMetadataSample
             inMetadataFactorList:   sleuth_inMetadataFactorList

runs/isaSampleToRawDataSeq/run.cwl

 cwlVersion: v1.2
 class: Workflow
 
+requirements:
+  MultipleInputFeatureRequirement: {}
+
 inputs:
   arcPath: Directory 
   assayName: string
@@ -15,10 +18,14 @@ steps:
       assayName: assayName
       startingNodeNum: startingNodeNum
       outName: outName
-    out: [output]
+    out:
+      - sampleseqCsv
+      - sampleseqXlsx
 
 outputs:
-  output: 
+  sampleseqs: 
     type: File[]
-    outputSource: isaSampleToRawDataSeq/output
+    outputSource:      
+      - isaSampleToRawDataSeq/sampleseqCsv
+      - isaSampleToRawDataSeq/sampleseqXlsx
 

runs/kallisto/run.cwl

@@ -35,9 +35,9 @@ steps:
       StandardDeviation: StandardDeviation
       BootstrapSamples: BootstrapSamples
       resultsFolder: resultsFolder
-    out: [finalOut]
+    out: [kallistoOutDir]
 
 outputs:
-  finalOut:
-    type: Directory[]
-    outputSource: kallisto/finalOut
+  kallistoOutDir:
+    type: Directory
+    outputSource: kallisto/kallistoOutDir

workflows/isaSampleToRawDataSeq/workflow.cwl

@@ -39,9 +39,13 @@ inputs:
       position: 4
 
 outputs:
-  output:
-    type: File[]
+  sampleseqCsv:
+    type: File
     outputBinding:
       glob:
         - "*.csv"
+  sampleseqXlsx:
+    type: File
+    outputBinding:
+      glob:
         - "*.xlsx"

workflows/kallisto/yield-dirInDestination.cwl → workflows/kallisto/gather-dirs.cwl

 cwlVersion: v1.2
 class: ExpressionTool
 doc: |
-  Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
+  Takes an array of directories (e.g. from a workflow step) and yields them in a destination directory.
 requirements:
   - class: InlineJavascriptRequirement
 inputs:
-  inDir: Directory
+  inDirs: Directory[]
   destinationDir: string
 expression: |
   ${
     return {"outDir": {
       "class": "Directory", 
       "basename": inputs.destinationDir,
-      "listing": [inputs.inDir]
+      "listing": inputs.inDirs
     } };
   }
 outputs:

workflows/kallisto/kallisto-quant.cwl

@@ -126,7 +126,7 @@ arguments: [ "--output-dir", $(inputs.QuantOutfolder) ]
 
 outputs:
 
-  outFolder:
+  kallistoQuantOutDir:
     type: Directory
     outputBinding:
       glob: $(runtime.outdir)/$(inputs.QuantOutfolder)

workflows/kallisto/workflow.cwl

@@ -51,17 +51,16 @@ steps:
             FragmentLength: FragmentLength
             StandardDeviation: StandardDeviation
             BootstrapSamples: BootstrapSamples
-        out: [outFolder]
-
+        out: [kallistoQuantOutDir]
     collectResults:
-        run: ./yield-dirInDestination.cwl
-        scatter: inDir
+        run: ./gather-dirs.cwl
         in:
-            inDir: quant/outFolder
+            inDirs: quant/kallistoQuantOutDir
             destinationDir: resultsFolder
         out: [outDir]
 
 outputs:
-  finalOut:
-    type: Directory[]
+  kallistoOutDir:
+    type: Directory
     outputSource: collectResults/outDir
+