Merge pull request #561 from MaxUlysse/MinorTweaks

Minor tweaks

Author: maxulysse

scripts/do_all.sh

@@ -4,13 +4,19 @@ set -xeuo pipefail
 PROFILE=singularity
 PUSH=''
 REPOSITORY=maxulysse
+GENOME=GRCh38
 TAG=latest
 TOOL=docker
 
 while [[ $# -gt 0 ]]
 do
     key=$1
     case $key in
+        --genome)
+        GENOME=$2
+        shift # past argument
+        shift # past value
+        ;;
         -p|--profile)
         PROFILE=$2
         shift # past argument
@@ -40,10 +46,19 @@ do
     esac
 done
 
-if [ $TOOL = docker ]
+if [ $GENOME = smallGRCh37 ]
+then
+    $GENOME = GRCh37
+fi
+
+function toLower() {
+    echo $1 | tr '[:upper:]' '[:lower:]'
+}
+
+if [ $TOOL = docker ] && [ GRCh37,GRCh38 =~ $GENOME ]
 then
     nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 fi