From e0b3cc46f51e573a92d1d1facfe1760e7230cd72 Mon Sep 17 00:00:00 2001
From: Chelsey <cfang@bsgsc.ca>
Date: Wed, 21 Jun 2017 15:06:29 -0700
Subject: [PATCH] Added generation of methylation bigWIGS to preprocess
 workflow

---
 cwl/tools/preprocess.cwl | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/cwl/tools/preprocess.cwl b/cwl/tools/preprocess.cwl
index 201ff26..8bf4a4c 100644
--- a/cwl/tools/preprocess.cwl
+++ b/cwl/tools/preprocess.cwl
@@ -12,7 +12,12 @@ outputs:
   combined: 
     type: File
     outputSource: mergeSymmetric/combined
-
+  methBW:
+    type: File
+    outputSource: methylationBigWIG/methBW
+  covBW:
+    type: File
+    outputSource: methylationBigWIG/covBW
 
 steps:
   convertMethylation:
@@ -25,3 +30,9 @@ steps:
     in:
       toCombine: convertMethylation/converted
     out: [combined]
+  methylationBigWIG:
+    run: methToBigWig.cwl
+    in: 
+      toConvert: mergeSymmetric/combined
+    out: [methBW, covBW]
+