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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 97461ce437f510061ced436eaf19e9bea7155669..183bca14f6cc6772f3803b29079f27d1ed7f34af 100644
(file)
--- a/
RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/
RNA-Seq/cwl/RNA-seq-wf.cwl
@@
-1,18
+1,26
@@
cwlVersion: v1.2
class: Workflow
cwlVersion: v1.2
class: Workflow
-label: RNAseq
CWL practice
workflow
+label: RNAseq workflow
inputs:
inputs:
- fq: File[]
+ fqdir:
+ type: Directory
+ loadListing: shallow_listing
genome: Directory
gtf: File
steps:
genome: Directory
gtf: File
steps:
+ splitDir:
+ in:
+ fqdir: fqdir
+ run: helper/splitDir.cwl
+ out: [fq]
+
alignment:
alignment:
- run: alignment.cwl
+ run:
helper/
alignment.cwl
scatter: fq
in:
scatter: fq
in:
- fq: fq
+ fq:
splitDir/
fq
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
genome: genome
gtf: gtf
out: [qc_html, bam_sorted_indexed]
@@
-21,17
+29,16
@@
steps:
requirements:
ResourceRequirement:
ramMin: 500
requirements:
ResourceRequirement:
ramMin: 500
- run: featureCounts.cwl
+ run:
helper/
featureCounts.cwl
in:
counts_input_bam: alignment/bam_sorted_indexed
gtf: gtf
out: [featurecounts]
in:
counts_input_bam: alignment/bam_sorted_indexed
gtf: gtf
out: [featurecounts]
- ### 2. Organizing output files into Directories
output-subdirs:
output-subdirs:
- run: subdirs.cwl
+ run:
helper/
subdirs.cwl
in:
in:
- fq: fq
+ 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]
@@
-48,3
+55,4
@@
outputs:
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
+ StepInputExpressionRequirement: {}