cwlVersion: v1.2
class: Workflow
-label: RNAseq CWL practice workflow
+label: RNAseq workflow
inputs:
- fq: File[]
+ fqdir:
+ type: Directory
+ loadListing: shallow_listing
genome: Directory
gtf: File
steps:
+ splitDir:
+ in:
+ fqdir: fqdir
+ run: helper/splitDir.cwl
+ out: [fq]
+
alignment:
- run: alignment.cwl
+ run: helper/alignment.cwl
scatter: fq
in:
- fq: fq
+ fq: splitDir/fq
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
requirements:
ResourceRequirement:
ramMin: 500
- run: featureCounts.cwl
+ run: helper/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
+ run: helper/subdirs.cwl
in:
- fq: fq
+ fq: splitDir/fq
bams: alignment/bam_sorted_indexed
qc: alignment/qc_html
out: [dirs]
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
+ StepInputExpressionRequirement: {}