cwlVersion: v1.2
class: Workflow
-label: RNAseq CWL practice workflow
+label: RNAseq workflow
inputs:
- fq: File[]
+ fqdir: Directory
genome: Directory
gtf: File
run: helper/alignment.cwl
scatter: fq
in:
- fq: fq
+ fq:
+ valueFrom: $(inputs.fq.listing)
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
output-subdirs:
run: helper/subdirs.cwl
in:
- fq: fq
+ fq:
+ valueFrom: $(inputs.fq.listing)
bams: alignment/bam_sorted_indexed
qc: alignment/qc_html
out: [dirs]
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
+
+hints:
+ LoadListingRequirement:
+ loadListing: shallow_listing