Fix Vep

.travis.yml

@@ -15,18 +15,19 @@ env:
   global:
     - NXF_VER=0.31.0 SGT_VER=2.4.2
   matrix:
-    - PROFILE=singularity TEST=TOOLS          TOOL_INSTALL=all
-    - PROFILE=singularity TEST=MANTA          TOOL_INSTALL=all
-    - PROFILE=docker      TEST=MANTA          TOOL_INSTALL=nextflow
-    - PROFILE=docker      TEST=TOOLS          TOOL_INSTALL=nextflow
-    - PROFILE=docker      TEST=ANNOTATEVEP    TOOL_INSTALL=nextflow
-    - PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
-    - PROFILE=singularity TEST=STEP           TOOL_INSTALL=all
-    - PROFILE=singularity TEST=GERMLINE       TOOL_INSTALL=all
-    - PROFILE=singularity TEST=DIR            TOOL_INSTALL=all
-    - PROFILE=docker      TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
-    - PROFILE=docker      TEST=STEP           TOOL_INSTALL=nextflow
-    - PROFILE=docker      TEST=GERMLINE       TOOL_INSTALL=nextflow
+    - PROFILE=singularity TEST=TOOLS          TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=singularity TEST=MANTA          TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=docker      TEST=MANTA          TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=docker      TEST=TOOLS          TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=docker      TEST=ANNOTATEVEP    TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=singularity TEST=STEP           TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=singularity TEST=GERMLINE       TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=singularity TEST=DIR            TOOL_INSTALL=all      TAG=2.1.0
+    - PROFILE=docker      TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=docker      TEST=STEP           TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=docker      TEST=GERMLINE       TOOL_INSTALL=nextflow TAG=2.1.0
+    - PROFILE=docker      TEST=DIR            TOOL_INSTALL=nextflow TAG=2.1.0
     - PROFILE=docker      TEST=DIR            TOOL_INSTALL=nextflow
 
 install: # Install Nextflow (and Singularity if needed)

annotate.nf

@@ -228,7 +228,7 @@ process RunVEP {
   finalannotator = annotator == "snpeff" ? 'merge' : 'vep'
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
   """
-  vep --dir /opt/vep/.vep/ \
+  vep \
   -i ${vcf} \
   -o ${vcf.simpleName}_VEP.ann.vcf \
   --assembly ${genome} \

scripts/test.sh

@@ -6,6 +6,7 @@ KEEP=false
 GENOME=smallGRCh37
 PROFILE=singularity
 SAMPLE=Sarek-data/testdata/tsv/tiny.tsv
+TAG=latest
 TEST=ALL
 TRAVIS=${TRAVIS:-false}
 
@@ -25,6 +26,11 @@ while [[ $# -gt 0 ]]
 do
   key=$1
   case $key in
+    -a|--tag)
+    TAG=$2
+    shift # past argument
+    shift # past value
+    ;;
     -g|--genome)
     GENOME=$2
     shift # past argument
@@ -60,7 +66,7 @@ do
 done
 
 function run_wrapper() {
-  ./scripts/wrapper.sh $@ --profile $PROFILE --genome $GENOME --genomeBase $PWD/References/$GENOME --verbose
+  ./scripts/wrapper.sh $@ --profile $PROFILE --genome $GENOME --genomeBase $PWD/References/$GENOME --verbose --TAG $TAG
 }
 
 function clean_repo() {