Moving to directory

no issue #
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>

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
-label: RNAseq CWL practice workflow
+label: RNAseq workflow 
 
 inputs:
-  fq: File[]
+  fqdir: Directory 
   genome: Directory
   gtf: File
 
@@ -12,7 +12,8 @@ steps:
     run: helper/alignment.cwl
     scatter: fq
     in:
-      fq: fq
+      fq:
+        valueFrom: $(inputs.fq.listing)
       genome: genome
       gtf: gtf
     out: [qc_html, bam_sorted_indexed]
@@ -30,7 +31,8 @@ steps:
   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]
@@ -47,3 +49,7 @@ outputs:
 requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
+
+hints:
+  LoadListingRequirement:
+    loadListing: shallow_listing

diff --git a/RNA-Seq/cwl/helper/alignment.cwl b/RNA-Seq/cwl/helper/alignment.cwl
index e2a434fe3f3852f3e1771d16f2d908b4ee059c55..702ba05b8a0d454f81def6d9e088c517cc91e8b8 100644 (file)
--- a/RNA-Seq/cwl/helper/alignment.cwl
+++ b/RNA-Seq/cwl/helper/alignment.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.2
 class: Workflow
-label: RNAseq CWL practice workflow
+label: RNAseq Alignment workflow
 
 inputs:
   fq: File