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Add splitDir to take Directory input
[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 cb00e167719a37d2f2b09c88e44fd92194f64fdd..183bca14f6cc6772f3803b29079f27d1ed7f34af 100644
(file)
--- a/
RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/
RNA-Seq/cwl/RNA-seq-wf.cwl
@@
-1,21
+1,26
@@
cwlVersion: v1.2
class: Workflow
cwlVersion: v1.2
class: Workflow
-label: RNAseq workflow
+label: RNAseq workflow
inputs:
inputs:
- fqdir:
- type: Directory
+ fqdir:
+ type: Directory
loadListing: shallow_listing
genome: Directory
gtf: File
steps:
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:
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]
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
@@
-33,8
+38,7
@@
steps:
output-subdirs:
run: helper/subdirs.cwl
in:
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]
bams: alignment/bam_sorted_indexed
qc: alignment/qc_html
out: [dirs]