From 527f6d896e17e098dfd3790e98bc5b609f35ac7f Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 10 Apr 2018 14:33:18 +0200
Subject: [PATCH 1/2] no need to build containers for both genome versions

---
 scripts/do_all.sh | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index 56f42821c3..597c11e21a 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -4,6 +4,7 @@ set -xeuo pipefail
 PROFILE=singularity
 PUSH=''
 REPOSITORY=maxulysse
+GENOME=GRCh38
 TAG=latest
 TOOL=docker
 
@@ -11,6 +12,11 @@ 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 controlfreec,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff,vcftools,vep
+    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 ${TAG} --containerPath containers/ --containers controlfreec,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vcftools,vep$(toLower ${GENOME})
 fi

From d38420e8d524ae1b661cafaa46caa76c2001a98c Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 10 Apr 2018 16:00:29 +0200
Subject: [PATCH 2/2] remove containers that does not exist yet

---
 scripts/do_all.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index 597c11e21a..e53acc23c5 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -57,8 +57,8 @@ function toLower() {
 
 if [ $TOOL = docker ] && [ GRCh37,GRCh38 =~ $GENOME ]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers controlfreec,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff,vcftools,vep
+    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 ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers controlfreec,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vcftools,vep$(toLower ${GENOME})
+    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