Updating for proper loadListing

[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 07386c1b5841d57c3a4316a70ab0179aa9125012..cb00e167719a37d2f2b09c88e44fd92194f64fdd 100644 (file)
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -3,7 +3,9 @@ class: Workflow
 label: RNAseq workflow 
 
 inputs:
-  fqdir: Directory 
+  fqdir: 
+    type: Directory 
+    loadListing: shallow_listing
   genome: Directory
   gtf: File
 
@@ -13,7 +15,7 @@ steps:
     scatter: fq
     in:
       fq:
-        valueFrom: $(inputs.fq.listing)
+        valueFrom: $(inputs.fqdir.listing)
       genome: genome
       gtf: gtf
     out: [qc_html, bam_sorted_indexed]
@@ -32,7 +34,7 @@ steps:
     run: helper/subdirs.cwl
     in:
       fq: 
-       valueFrom: $(inputs.fq.listing)
+       valueFrom: $(inputs.fqdir.listing)
       bams: alignment/bam_sorted_indexed
       qc: alignment/qc_html
     out: [dirs]
@@ -49,7 +51,4 @@ outputs:
 requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
-
-hints:
-  LoadListingRequirement:
-    loadListing: shallow_listing
+  StepInputExpressionRequirement: {}