Arc cwl

arc.cwl

+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  #### runs/kallisto
+  kallisto_IndexInput: File[]
+  kallisto_sampleRecord:
+    type:
+      type: array
+      items:
+        type: record
+        fields:
+          readsOfOneSample:
+            type: File[]
+          sampleName:
+            type: string?
+  kallisto_isSingle: boolean
+  kallisto_FragmentLength: double?  
+  kallisto_StandardDeviation: double?
+  kallisto_BootstrapSamples: int?
+  kallisto_resultsFolder: string
+
+  #### runs/isaSampleToRawDataSeq
+  isaSampleToRawDataSeq_arcPath: Directory 
+  isaSampleToRawDataSeq_assayName: string
+  isaSampleToRawDataSeq_startingNodeNum: int
+  isaSampleToRawDataSeq_outName: string
+
+  #### runs/sleuth
+#   sleuth_inKallistoResults: Directory
+#   sleuth_inMetadataFile: File
+  sleuth_inMetadataSample: string
+  sleuth_inMetadataFactorList: string[]
+  sleuth_inMetadataDataCol: string
+  sleuth_outFolder: string
+
+steps:
+    kallisto:
+        run: runs/kallisto/run.cwl
+        in:
+            IndexInput:         kallisto_IndexInput
+            sampleRecord:       kallisto_sampleRecord
+            isSingle:           kallisto_isSingle
+            FragmentLength:     kallisto_FragmentLength
+            StandardDeviation:  kallisto_StandardDeviation
+            BootstrapSamples:   kallisto_BootstrapSamples
+            resultsFolder:      kallisto_resultsFolder
+        out: [kallistoOutDir]
+
+
+    isaSampleToRawDataSeq:
+        run: runs/isaSampleToRawDataSeq/run.cwl
+        in:
+          arcPath:          isaSampleToRawDataSeq_arcPath
+          assayName:        isaSampleToRawDataSeq_assayName
+          startingNodeNum:  isaSampleToRawDataSeq_startingNodeNum
+          outName:          isaSampleToRawDataSeq_outName
+        out: [sampleseqCsv, sampleseqXlsx]
+
+    sleuth:
+        run: runs/sleuth/run.cwl
+        in:
+            inKallistoResults:      kallisto/kallistoOutDir
+            inMetadataFile:         isaSampleToRawDataSeq/sampleseqCsv
+            inMetadataSample:       sleuth_inMetadataSample
+            inMetadataFactorList:   sleuth_inMetadataFactorList
+            inMetadataDataCol:      sleuth_inMetadataDataCol
+            outFolder:              sleuth_outFolder
+        out: [outdir]
+
+outputs:
+
+  outdir:
+    type: Directory[]
+    outputSource: sleuth/outdir
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