Migrating to carpentries WIP

[rnaseq-cwl-training.git] / answers / ep6 / main.cwl

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+cwlVersion: v1.2
+class: Workflow
+label: RNAseq CWL practice workflow
+
+inputs:
+  fq: File[]
+  genome: Directory
+  gtf: File
+
+steps:
+  alignment:
+    run: alignment.cwl
+    scatter: fq
+    in:
+      fq: fq
+      genome: genome
+      gtf: gtf
+    out: [qc_html, bam_sorted_indexed]
+
+  featureCounts:
+    requirements:
+      ResourceRequirement:
+        ramMin: 500
+    run: featureCounts.cwl
+    in:
+      counts_input_bam: alignment/bam_sorted_indexed
+      gtf: gtf
+    out: [featurecounts]
+
+  ### 2. Organizing output files into Directories
+  output-subdirs:
+    run: subdirs.cwl
+    in:
+      fq: fq
+      bams: alignment/bam_sorted_indexed
+      qc: alignment/qc_html
+    out: [dirs]
+
+outputs:
+  dirs:
+    type: Directory[]
+    outputSource: output-subdirs/dirs
+
+  featurecounts:
+    type: File
+    outputSource: featureCounts/featurecounts
+
+requirements:
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}