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 555e5e2cc1aa17875ff56141b68060af96ac5bdd..183bca14f6cc6772f3803b29079f27d1ed7f34af 100644 (file)
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -1,19 +1,26 @@
 cwlVersion: v1.2
 class: Workflow
-label: RNAseq workflow 
+label: RNAseq workflow
 
 inputs:
-  fqdir: 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]
@@ -31,8 +38,7 @@ steps:
   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]
@@ -50,7 +56,3 @@ requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
   StepInputExpressionRequirement: {}
-
-hints:
-  LoadListingRequirement:
-    loadListing: shallow_listing