From 230f9ba156ba4ba0fd804179c7a1007ee8bd0fa5 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Wed, 13 Sep 2017 23:32:21 -0400
Subject: [PATCH 1/2] output argument name change for pairsam

---
 cwl_awsem/pairsam-parse-sort.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cwl_awsem/pairsam-parse-sort.cwl b/cwl_awsem/pairsam-parse-sort.cwl
index 222817e..15649aa 100755
--- a/cwl_awsem/pairsam-parse-sort.cwl
+++ b/cwl_awsem/pairsam-parse-sort.cwl
@@ -70,7 +70,7 @@
                 "null",
                 "File"
             ],
-            "id": "#out_pairs"
+            "id": "#out_pairsam"
         }
     ],
     "cwlVersion": "draft-3",

From 88ab08eee3c2e5b5dc5f8241e1cef71839667a69 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Thu, 14 Sep 2017 00:25:22 -0400
Subject: [PATCH 2/2] added outdir to pairsam-parse-sort

---
 cwl_awsem/pairsam-parse-sort.cwl | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/cwl_awsem/pairsam-parse-sort.cwl b/cwl_awsem/pairsam-parse-sort.cwl
index 15649aa..4ef5761 100755
--- a/cwl_awsem/pairsam-parse-sort.cwl
+++ b/cwl_awsem/pairsam-parse-sort.cwl
@@ -21,10 +21,22 @@
             ],
             "inputBinding": {
                 "separate": true,
-                "position": 3
+                "position": 2
             },
             "id": "#chromsize"
         },
+        {
+            "default": ".",
+            "type": [
+                "null",
+                "string"
+            ],
+            "inputBinding": {
+                "separate": true,
+                "position": 3
+            },
+            "id": "#outdir"
+        },
         {
             "default": "out",
             "type": [
@@ -33,7 +45,7 @@
             ],
             "inputBinding": {
                 "separate": true,
-                "position": 2
+                "position": 4
             },
             "id": "#outprefix"
         },
@@ -43,7 +55,7 @@
             ],
             "id": "#Threads",
             "inputBinding": {
-                "position": 4,
+                "position": 5,
                 "separate": true
             },
             "default": 8
@@ -55,7 +67,7 @@
             ],
             "inputBinding": {
                 "separate": true,
-                "position": 5
+                "position": 6
             },
             "id": "#compress_programm"
         },