Merge branch 'release/2.0.0'

cancerit · Feb 26, 2018 · ca20858 · ca20858
2 parents da0d188 + f05f651
commit ca20858
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Showing 9 changed files with 31 additions and 5 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 2.0.0
+
+* Update to use [cgpBigWig-1.0.0](https://github.com/cancerit/cgpBigWig/releases/tag/1.0.0)
+* Add `--overlap` support to appropriate cwls `bam2bedgraph` `bam2bw` `bam2bwbases`
+
 ## 1.0.0
 
 * First container release uses [cgpBigWig-0.5.0](https://github.com/cancerit/cgpBigWig/releases/tag/0.5.0)

diff --git a/Dockerfile b/Dockerfile
@@ -36,7 +36,7 @@ FROM  ubuntu:16.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="1.0.0" \
+      version="2.0.0" \
       description="cgpBigWig for dockstore.org"
 
 ENV OPT /opt/wtsi-cgp

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -10,7 +10,7 @@ set -u
 
 VER_HTSLIB="1.7"
 VER_LIBBW="0.4.2"
-VER_CGPBIGWIG="0.5.0"
+VER_CGPBIGWIG="1.0.0"
 
 if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path such as /opt/ICGC"

diff --git a/cwls/bam2bedgraph.cwl b/cwls/bam2bedgraph.cwl
@@ -45,6 +45,11 @@ inputs:
     doc: "Ignore reads with the filter flags"
     inputBinding:
       prefix: --filter
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
 
 outputs:
   output:

diff --git a/cwls/bam2bw.cwl b/cwls/bam2bw.cwl
@@ -59,6 +59,11 @@ inputs:
     - .fai
     inputBinding:
       prefix: --reference
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
 
 outputs:
   output:

diff --git a/cwls/bam2bwbases.cwl b/cwls/bam2bwbases.cwl
@@ -51,6 +51,11 @@ inputs:
     type: File?
     inputBinding:
       prefix: --reference
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
 
 
 outputs:

diff --git a/examples/bam2bedgraph.json b/examples/bam2bedgraph.json
@@ -4,5 +4,7 @@
     "class": "File"
   },
 
-  "filter": 3852
+  "filter": 3852,
+
+  "overlap": false
 }
diff --git a/examples/bam2bw.json b/examples/bam2bw.json
@@ -9,6 +9,8 @@
   "reference": {
     "path": "/your/path/to/GRCh37d5/genome.fa",
     "class": "File"
-  }
+  },
+
+  "overlap": false
 
 }
diff --git a/examples/bam2bwbases.json b/examples/bam2bwbases.json
@@ -14,5 +14,7 @@
   "output_path": {
     "path": "bam2bwbases.out.bw",
     "class": "File"
-  }
+  },
+
+  "overlap": false
 }