Merge branch 'hotfix/3.1.1'

cancerit · Apr 8, 2019 · 6e0224a · 6e0224a
2 parents 589c766 + 2f67a30
commit 6e0224a
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,13 @@
 # CHANGES
 
+## 3.1.1
+
+* Update to dockstore-cgpmap:3.1.1 for base image
+* Bump vcftools to 0.1.16 - security
+* Allow jobs to resume when process scripts exist, long since proven double run doesn't occur
+* Ensure that ENA server is never used for CRAM processing
+* New versio of cgpCaVEManPostProcessing to solve memory problems in flagging when using BED files, also bumps vcftools
+
 ## 3.1.0
 
 * Update to dockstore-cgpmap:3.1.0 for base image

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:3.1.0 as builder
+FROM  quay.io/wtsicgp/dockstore-cgpmap:3.1.1 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="3.1.0"
+LABEL uk.ac.sanger.cgp.version="3.1.1"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends\

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -10,13 +10,13 @@ set -u
 
 # cgpVcf
 VER_CGPVCF="v2.2.1"
-VER_VCFTOOLS="0.1.15"
+VER_VCFTOOLS="0.1.16"
 
 # cgpPindel
 VER_CGPPINDEL="v3.1.2"
 
 # cgpCaVEManPostProcessing
-VER_CGPCAVEPOSTPROC="1.8.6"
+VER_CGPCAVEPOSTPROC="1.8.7"
 # if issues found downgrade to 2.23.0 but can't find any use of bedtools coverage
 VER_BEDTOOLS="2.27.1"
 

diff --git a/cwls/cgpwxs.cwl b/cwls/cgpwxs.cwl
@@ -24,7 +24,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.1.0"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.1.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/scripts/analysisWXS.sh b/scripts/analysisWXS.sh
@@ -131,7 +131,7 @@ if [ "$ALN_EXTN" == "cram" ]; then
   ## prime the cache
   USER_CACHE=$OUTPUT_DIR/ref_cache
   export REF_CACHE=$USER_CACHE/%2s/%2s/%s
-  export REF_PATH=$REF_CACHE:http://www.ebi.ac.uk/ena/cram/md5/%s
+  export REF_PATH=$REF_CACHE
   do_parallel[cache_POP]="seq_cache_populate.pl -root $USER_CACHE $REF_BASE/genome.fa"
 fi
 

diff --git a/scripts/ds-cgpwxs.pl b/scripts/ds-cgpwxs.pl
@@ -70,7 +70,6 @@
 my $run_file = $opts{'o'}.'/run.params';
 open my $FH,'>',$run_file or die "Failed to write to $run_file: $!";
 # Force explicit checking of file flush
-print $FH "export PCAP_THREADED_NO_SCRIPT=1\n";
 print $FH "export PCAP_THREADED_FORCE_SYNC=1\n";
 print $FH "export PCAP_THREADED_LOADBACKOFF=1\n";
 print $FH "export PCAP_THREADED_REM_LOGS=1\n";