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Moving to directory
[arvados-tutorial.git]
/
RNA-Seq
/
cwl
/
RNA-seq-wf.cwl
diff --git
a/RNA-Seq/cwl/RNA-seq-wf.cwl
b/RNA-Seq/cwl/RNA-seq-wf.cwl
index 8da505cd8bb507ae0c6829860954ffcdccb1b61d..07386c1b5841d57c3a4316a70ab0179aa9125012 100644
(file)
--- a/
RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/
RNA-Seq/cwl/RNA-seq-wf.cwl
@@
-1,9
+1,9
@@
cwlVersion: v1.2
class: Workflow
cwlVersion: v1.2
class: Workflow
-label: RNAseq
CWL practice workflow
+label: RNAseq
workflow
inputs:
inputs:
- fq
: File[]
+ fq
dir: Directory
genome: Directory
gtf: File
genome: Directory
gtf: File
@@
-12,7
+12,8
@@
steps:
run: helper/alignment.cwl
scatter: fq
in:
run: helper/alignment.cwl
scatter: fq
in:
- fq: fq
+ fq:
+ valueFrom: $(inputs.fq.listing)
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
@@
-30,7
+31,8
@@
steps:
output-subdirs:
run: helper/subdirs.cwl
in:
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]
bams: alignment/bam_sorted_indexed
qc: alignment/qc_html
out: [dirs]
@@
-47,3
+49,7
@@
outputs:
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
+
+hints:
+ LoadListingRequirement:
+ loadListing: shallow_listing