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Minor tweaks #561

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merged 3 commits into from
Apr 10, 2018
Merged

Minor tweaks #561

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c2ce455
no need to build containers for both genome versions
maxulysse Apr 10, 2018
0aafed8
remove containers that does not exist yet
maxulysse Apr 10, 2018
0ac5305
Merge remote-tracking branch 'upstream/master' into MinorTweaks
maxulysse Apr 10, 2018
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21 changes: 18 additions & 3 deletions scripts/do_all.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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