Merge pull request #10 from 4dn-dcic/dev

Dev
4dn-dcic · Sep 14, 2017 · 54b6309 · 54b6309
2 parents d555212 + 3a7f291
commit 54b6309
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Showing 5 changed files with 30 additions and 7 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -2,6 +2,7 @@ sudo: false
 language: python
 env:
   - BENCHMARK_TEST=1
+  - CWL_NAME=pairsam-parse-sort
   - CWL_NAME=extract-mcool-normvector-for-juicebox
   - CWL_NAME=md5
   - CWL_NAME=fastqc-0-11-4-1
@@ -10,7 +11,6 @@ env:
   - CWL_NAME=hi-c-processing-partc
   - CWL_NAME=bwa-mem
 python:
-  - '3.5'
   - '2.7'
 os:
   - linux

diff --git a/Benchmark/_version.py b/Benchmark/_version.py
@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "0.1.1"
+__version__ = "0.1.2"
diff --git 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"
         },
@@ -70,7 +82,7 @@
                 "null",
                 "File"
             ],
-            "id": "#out_pairs"
+            "id": "#out_pairsam"
         }
     ],
     "cwlVersion": "draft-3",

diff --git a/tests/test_files/test.bam b/tests/test_files/test.bam
diff --git a/tests/test_input_json/pairsam-parse-sort.input.json b/tests/test_input_json/pairsam-parse-sort.input.json
@@ -0,0 +1,11 @@
+{
+    "bam": {
+        "class": "File", 
+        "path": "../test_files/test.bam"
+    }, 
+    "chromsize": {
+        "class": "File", 
+        "path": "../test_files/hg38.mainonly.chrom.sizes"
+    }, 
+    "nThreads": 1
+}