Merge branch 'hotfix/3.0.2'

CHANGES.md

@@ -1,5 +1,12 @@
 # CHANGES
 
+## 3.0.2
+
+Bumps versions of dependencies to bring in
+
+* Official release of Bio-DB_HTS
+* Alternate use of tabix query to allow contigs with names containing colon.
+
 ## 3.0.1
 
 Updates to relating to:

Dockerfile

@@ -1,4 +1,4 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:3.0.2 as builder
+FROM  quay.io/wtsicgp/dockstore-cgpmap:3.0.3 as builder
 
 USER  root
 
@@ -33,7 +33,7 @@ MAINTAINER  cgphelp@sanger.ac.uk
 
 LABEL vendor="CASM/Cancer IT, Wellcome Sanger Institute"
 LABEL uk.ac.sanger.cgp.description="CGP WXS pipeline for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.0.1"
+LABEL uk.ac.sanger.cgp.version="3.0.2"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends\

build/opt-build.sh

@@ -13,10 +13,10 @@ VER_CGPVCF="v2.2.1"
 VER_VCFTOOLS="0.1.15"
 
 # cgpPindel
-VER_CGPPINDEL="v3.0.0"
+VER_CGPPINDEL="v3.0.1"
 
 # cgpCaVEManPostProcessing
-VER_CGPCAVEPOSTPROC="1.8.1"
+VER_CGPCAVEPOSTPROC="1.8.2"
 # if issues found downgrade to 2.23.0 but can't find any use of bedtools coverage
 VER_BEDTOOLS="2.27.1"
 
@@ -25,7 +25,7 @@ VER_CGPCAVEWRAP="1.13.2"
 VER_CAVEMAN="1.13.2"
 
 # VAGrENT
-VER_VAGRENT="v3.3.0"
+VER_VAGRENT="v3.3.2"
 
 if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path such as /opt/ICGC"

cwls/cgpwxs.cwl

@@ -24,7 +24,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.0.1"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.0.2"
 
 hints:
   - class: ResourceRequirement