Merge branch 'hotfix/1.0.6'

CHANGES.md

@@ -1,3 +1,7 @@
+### 1.0.6
+* Fixes #13 - Parsing of sample name from BAM headers fails is sample at end of line
+* Update dockstore-cgpwxs to [2.0.7](https://github.com/cancerit/dockstore-cgpwxs/releases/tag/2.0.7) - Fixes bug in pindel core.
+
 ### 1.0.5
 * Improved handling of CPU oversubscription via PCAP-core update in base image
 * Update cgpCaVEManWrapper to expose extra options (specifically split size)

Dockerfile

@@ -1,9 +1,9 @@
-FROM  quay.io/wtsicgp/dockstore-cgpwxs:2.0.6
+FROM  quay.io/wtsicgp/dockstore-cgpwxs:2.0.7
 
 MAINTAINER  [email protected]
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="1.0.5" \
+      version="1.0.6" \
       description="The CGP WGS pipeline for dockstore.org"
 
 USER  root

Dockstore.cwl

@@ -19,7 +19,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:1.0.5"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:1.0.6"
 
 hints:
   - class: ResourceRequirement

scripts/analysisWGS.sh

@@ -102,8 +102,8 @@ if [ ! -f $OUTPUT_DIR/pre-exec.done ]; then
 fi
 
 ## get sample names from BAM headers
-NAME_MT=`samtools view -H $BAM_MT | perl -ne 'if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
-NAME_WT=`samtools view -H $BAM_WT | perl -ne 'if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
+NAME_MT=`samtools view -H $BAM_MT | perl -ne 'chomp; if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
+NAME_WT=`samtools view -H $BAM_WT | perl -ne 'chomp; if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
 
 echo -e "\tNAME_MT : $NAME_MT"
 echo -e "\tNAME_WT : $NAME_WT"