Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
cwlVersion: v1.2
class: Workflow
-label: RNAseq workflow
+label: RNAseq workflow
inputs:
- fqdir:
- type: Directory
+ fqdir:
+ type: Directory
loadListing: shallow_listing
genome: Directory
gtf: File
steps:
+ splitDir:
+ in:
+ fqdir: fqdir
+ run: helper/splitDir.cwl
+ out: [fq]
+
alignment:
run: helper/alignment.cwl
scatter: fq
in:
- fq:
- valueFrom: $(inputs.fqdir.listing)
+ fq: splitDir/fq
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
output-subdirs:
run: helper/subdirs.cwl
in:
- fq:
- valueFrom: $(inputs.fqdir.listing)
+ fq: splitDir/fq
bams: alignment/bam_sorted_indexed
qc: alignment/qc_html
out: [dirs]
--- /dev/null
+cwlVersion: v1.2
+class: ExpressionTool
+requirements:
+ InlineJavascriptRequirement: {}
+inputs:
+ fqdir: Directory
+outputs:
+ fq: File[]
+expression: '${return {fq: inputs.fqdir.listing};}'
fqdir:
class: Directory
- location: keep:pirca-4zz18-blweknwtwyjys0i/
+ location: keep:1360b500543d1d0b041084a2f99d33b6+567/
+ #location: keep:pirca-4zz18-blweknwtwyjys0i/
genome:
class: Directory
- location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
+ location: keep:64e703acc21226ce99f3d88eacdacd0b+3159/hg19-STAR-index
+ #location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
gtf:
class: File
- location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf
-
+ location: keep:64e703acc21226ce99f3d88eacdacd0b+3159/chr1-hg19_genes.gtf
+ #location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf