--- /dev/null
+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: {}