From 39c468199d6abf46b16fdc55da6b1b784dad8ddc Mon Sep 17 00:00:00 2001
From: Jeltje <jeltje.van.baren@gmail.com>
Date: Tue, 12 Sep 2017 01:56:49 +0000
Subject: [PATCH] Changed CWL to specific per-file output instead of directory.
 This is necessary for running Dockstore on the Computational Genomics
 Platform at UCSC

---
 starfusion.cwl | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/starfusion.cwl b/starfusion.cwl
index 6bc9551..1b99d2d 100644
--- a/starfusion.cwl
+++ b/starfusion.cwl
@@ -5,6 +5,7 @@ label: "STAR-fusion workflow by Jacob Pfeil; CWL by Jeltje van Baren"
 cwlVersion: v1.0
 
 requirements:
+  - class: InlineJavascriptRequirement
   - class: DockerRequirement
     dockerPull: "ucsctreehouse/fusion:0.2.0"
 
@@ -76,11 +77,19 @@ inputs:
 
 outputs:
 
-  output:
-    type: Directory
+  output1:
+    type: File
     outputBinding:
-       glob: $(inputs.outputdir)
-
-
-
-
+       glob: $(inputs.outputdir+'/star-fusion-gene-list-filtered.final')
+  output2:
+    type: File
+    outputBinding:
+       glob: $(inputs.outputdir+'/star-fusion-gene-list-filtered.final.bedpe')
+  output3:
+    type: File
+    outputBinding:
+       glob: $(inputs.outputdir+'/star-fusion-non-filtered.final')
+  output4:
+    type: File
+    outputBinding:
+       glob: $(inputs.outputdir+'/star-fusion-non-filtered.final.bedpe')