Updating to take a directory

[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..555e5e2cc1aa17875ff56141b68060af96ac5bdd 100644 (file)
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -1,18 +1,19 @@
 cwlVersion: v1.2
 class: Workflow
-label: RNAseq CWL practice workflow
+label: RNAseq workflow 
 
 inputs:
-  fq: File[]
+  fqdir: Directory 
   genome: Directory
   gtf: File
 
 steps:
   alignment:
-    run: alignment.cwl
+    run: helper/alignment.cwl
     scatter: fq
     in:
-      fq: fq
+      fq:
+        valueFrom: $(inputs.fqdir.listing)
       genome: genome
       gtf: gtf
     out: [qc_html, bam_sorted_indexed]
@@ -21,17 +22,17 @@ steps:
     requirements:
       ResourceRequirement:
         ramMin: 500
-    run: featureCounts.cwl
+    run: helper/featureCounts.cwl
     in:
       counts_input_bam: alignment/bam_sorted_indexed
       gtf: gtf
     out: [featurecounts]
 
-  ### 2. Organizing output files into Directories
   output-subdirs:
-    run: subdirs.cwl
+    run: helper/subdirs.cwl
     in:
-      fq: fq
+      fq: 
+       valueFrom: $(inputs.fqdir.listing)
       bams: alignment/bam_sorted_indexed
       qc: alignment/qc_html
     out: [dirs]
@@ -48,3 +49,8 @@ outputs:
 requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+
+hints:
+  LoadListingRequirement:
+    loadListing: shallow_listing