diff --git a/README.md b/README.md
index e1b07997..10affd22 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
 <h1>NGS_DNA pipeline</h1>
+
 <h2>Manual</h2>
 Find manual on installation and use at https://molgenis.gitbooks.io/molgenis-pipelines/
 
@@ -7,6 +8,7 @@ The sequencer is producing reads (in FastQ format) and are aligned to the hg19 r
 Sambamba (Tarasov et al.<sup>2</sup>)  is processing the aligned reads and then we applied GATK (McKenna et al. <sup>3</sup>) duplicate removal,
 performed SNP and INDEL discovery and genotyping using standard hard filtering parameters to GATK Best Practices recommendations (Van der Auwera et al.<sup>4</sup>)
 
+
 <h3>References</h3>
 1. Li Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform.
 2. Sambamba: Fast processing of NGS alignment formats
diff --git a/generate_template.sh b/generate_template.sh
index a51ee452..c5d6b4a0 100755
--- a/generate_template.sh
+++ b/generate_template.sh
@@ -1,94 +1,109 @@
 #!/bin/bash
 
 module load NGS_DNA/3.4.1
-module list 
-HOST=$(hostname -s)
-thisDir=$(pwd)
+module list
+host=$(hostname -s)
+environmentParameters="parameters_${host}"
+
+function showHelp() {
+	#
+	# Display commandline help on STDOUT.
+	#
+	cat <<EOH
+===============================================================================================================
+Script to copy (sync) data from a succesfully finished analysis project from tmp to prm storage.
+Usage:
+	$(basename $0) OPTIONS
+Options:
+	-h   Show this help.
+	-a   sampleType (DNA or RNA) (default=DNA)
+	-b   build (default=b37)
+	-c   batch (_chr or _small) (default=_chr)
+	-g   group (default=basename of ../../../ )
+	-p   project (default=basename of this directory)
+	-r   runID (default=run01)
+	-s   species (default=homo_sapiens)
+	-t   tmpDirectory (default=basename of ../../ )
+	-w   workdir (default=/groups/\${group}/\${tmpDirectory})
+
+===============================================================================================================
+EOH
+	trap - EXIT
+	exit 0
+}
+
+
+while getopts "t:g:w:p:r:s:b:c:h" opt; 
+do
+	case $opt in h)showHelp;; t)tmpDirectory="${OPTARG}";; g)group="${OPTARG}";; w)workDir="${OPTARG}";; p)project="${OPTARG}";; r)runID="${OPTARG}";; s)species="${OPTARG}";; b)build="${OPTARG}";; c)batch="${OPTARG}";; 
+	esac 
+done
+
+if [[ -z "${tmpDirectory:-}" ]]; then tmpDirectory=$(basename $(cd ../../ && pwd )) ; fi ; echo "tmpDirectory=${tmpDirectory}"
+if [[ -z "${group:-}" ]]; then group=$(basename $(cd ../../../ && pwd )) ; fi ; echo "group=${group}"
+if [[ -z "${workDir:-}" ]]; then workDir="/groups/${group}/${tmpDirectory}" ; fi ; echo "workDir=${workDir}"
+if [[ -z "${project:-}" ]]; then project=$(basename $(pwd )) ; fi ; echo "project=${project}"
+if [[ -z "${runID:-}" ]]; then runID="run01" ; fi ; echo "runID=${runID}"
+if [[ -z "${species:-}" ]]; then species="homo_sapiens" ; fi ; echo "species=${species}"
+if [[ -z "${build:-}" ]]; then build="b37" ; fi ; echo "build=${build}"
+if [[ -z "${batch:-}" ]]; then batch="_chr"; fi ; echo "batch=${batch}"
 
-ENVIRONMENT_PARAMETERS="parameters_${HOST}.csv"
-TMPDIRECTORY=$(basename $(cd ../../ && pwd ))
-GROUP=$(basename $(cd ../../../ && pwd ))
-
-PROJECT=projectXX
-WORKDIR="/groups/${GROUP}/${TMPDIRECTORY}"
-RUNID=runXX
-SPECIES="homo_sapiens"
-BUILD="b37"
 
 ## Normal user, please leave BATCH at _chr
 ## For expert modus: small batchsize (6) fill in '_small'  or per chromosome fill in _chr
-BATCH="_chr"
-
-GENSCRIPTS="${WORKDIR}/generatedscripts/${PROJECT}"
 
-samplesheet=${GENSCRIPTS}/${PROJECT}.csv
-mac2unix $samplesheet
+genScripts="${workDir}/generatedscripts/${project}/"
+samplesheet="${genScripts}/${project}.csv" ; mac2unix "${samplesheet}"
 
-python ${EBROOTNGS_DNA}/scripts/samplesize.py ${samplesheet} $thisDir
-SAMPLESIZE=$(cat externalSampleIDs.txt | uniq | wc -l)
+python "${EBROOTNGS_DNA}/scripts/samplesize.py" "${samplesheet}" $(pwd)
+sampleSize=$(cat externalSampleIDs.txt | uniq | wc -l)
+echo "Samplesize is ${sampleSize}"
 
-python ${EBROOTNGS_DNA}/scripts/gender.py $samplesheet
-var=$(cat ${samplesheet}.tmp | wc -l)
+python "${EBROOTNGS_DNA}/scripts/gender.py" "${samplesheet}"
+var=$(cat "${samplesheet}.tmp" | wc -l)
 
 
-if [ $var != 0 ]
+if [ "${var}" != 0 ]
 then
-    	mv ${samplesheet}.tmp ${samplesheet}
+	mv "${samplesheet}.tmp" "${samplesheet}"
         echo "samplesheet updated with Gender column"
 fi
-echo "Samplesize is $SAMPLESIZE"
 
-if [ $SAMPLESIZE -gt 199 ]
+if [ $sampleSize -gt 199 ]
 then
-    	WORKFLOW=${EBROOTNGS_DNA}/workflow_samplesize_bigger_than_200.csv
+	workflow=${EBROOTNGS_DNA}/workflow_samplesize_bigger_than_200.csv
 else
-        WORKFLOW=${EBROOTNGS_DNA}/workflow.csv
-fi
-
-if [ -f .compute.properties ];
-then
-     rm .compute.properties
-fi
-
-if [ -f ${GENSCRIPTS}/out.csv  ];
-then
-    	rm -rf ${GENSCRIPTS}/out.csv
+        workflow=${EBROOTNGS_DNA}/workflow.csv
 fi
 
-echo "tmpName,${TMPDIRECTORY}" > ${GENSCRIPTS}/tmpdir_parameters.csv 
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${GENSCRIPTS}/tmpdir_parameters.csv > \
-${GENSCRIPTS}/tmpdir_parameters_converted.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters.csv > \
-${GENSCRIPTS}/out.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters_${GROUP}.csv > \
-${GENSCRIPTS}/group_parameters.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/${ENVIRONMENT_PARAMETERS} > \
-${GENSCRIPTS}/environment_parameters.csv
-
-
-sh $EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh \
--p ${GENSCRIPTS}/out.csv \
--p ${GENSCRIPTS}/group_parameters.csv \
--p ${GENSCRIPTS}/environment_parameters.csv \
--p ${GENSCRIPTS}/tmpdir_parameters_converted.csv \
--p ${EBROOTNGS_DNA}/batchIDList${BATCH}.csv \
--p ${GENSCRIPTS}/${PROJECT}.csv \
--w ${EBROOTNGS_DNA}/create_in-house_ngs_projects_workflow.csv \
--rundir ${GENSCRIPTS}/scripts \
---runid ${RUNID} \
--o "workflowpath=${WORKFLOW};\
-outputdir=scripts/jobs;mainParameters=${GENSCRIPTS}/out.csv;\
-group_parameters=${GENSCRIPTS}/group_parameters.csv;\
-groupname=${GROUP};\
+if [ -f "${genScripts}/out.csv"  ];then rm -rf "${genScripts}/out.csv" ; fi
+
+echo "tmpName,${tmpDirectory}" > ${genScripts}/tmpdir_parameters.csv 
+perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${genScripts}/tmpdir_parameters.csv" > "${genScripts}/tmpdir_parameters_converted.csv"
+perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/parameters.csv" > "${genScripts}/out.csv"
+perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/parameters_${group}.csv" > "${genScripts}/group_parameters.csv"
+perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/${environmentParameters}.csv" > "${genScripts}/environment_parameters.csv"
+
+echo "BATCHIDLIST=${EBROOTNGS_DNA}/batchIDList${batch}.csv"
+
+sh "${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh" \
+-p "${genScripts}/out.csv" \
+-p "${genScripts}/group_parameters.csv" \
+-p "${genScripts}/environment_parameters.csv" \
+-p "${genScripts}/tmpdir_parameters_converted.csv" \
+-p "${EBROOTNGS_DNA}/batchIDList${batch}.csv" \
+-p "${genScripts}/${project}.csv" \
+-w "${EBROOTNGS_DNA}/create_in-house_ngs_projects_workflow.csv" \
+-rundir "${genScripts}/scripts" \
+--runid "${runID}" \
+-o workflowpath="${workflow};\
+outputdir=scripts/jobs;mainParameters=${genScripts}/out.csv;\
+group_parameters=${genScripts}/group_parameters.csv;\
+groupname=${group};\
 ngsversion=$(module list | grep -o -P 'NGS_DNA(.+)');\
-environment_parameters=${GENSCRIPTS}/environment_parameters.csv;\
-tmpdir_parameters=${GENSCRIPTS}/tmpdir_parameters_converted.csv;\
-batchIDList=${EBROOTNGS_DNA}/batchIDList${BATCH}.csv;\
-worksheet=${GENSCRIPTS}/${PROJECT}.csv" \
+environment_parameters=${genScripts}/environment_parameters.csv;\
+tmpdir_parameters=${genScripts}/tmpdir_parameters_converted.csv;\
+batchIDList=${EBROOTNGS_DNA}/batchIDList${batch}.csv;\
+worksheet=${genScripts}/${project}.csv" \
 -weave \
 --generate
-
diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
index b298fe7a..972a19b9 100755
--- a/protocols/CreateExternSamplesProjects.sh
+++ b/protocols/CreateExternSamplesProjects.sh
@@ -38,8 +38,8 @@ set -e
 set -u
 
 umask 0007
-module load $ngsUtilsVersion
-module load $ngsversion
+module load ${ngsUtilsVersion}
+module load ${ngsversion}
 
 module list
 #
diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
index 2eaebacc..29e7b134 100644
--- a/test/test_pipeline.sh
+++ b/test/test_pipeline.sh
@@ -57,23 +57,28 @@ cp generate_template.sh ${workfolder}/generatedscripts/PlatinumSubset/generate_t
 fgrep "computeVersion," parameters.csv > ${workfolder}/generatedscripts/PlatinumSubset/mcVersion.txt
 
 NGS_DNA_VERSION=NGS_DNA/3.4.1
-module load $NGS_DNA_VERSION
-perl -pi -e "s|module load $NGS_DNA_VERSION|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|" ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
-perl -pi -e 's|PROJECT=projectXX|PROJECT=PlatinumSubset|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
-perl -pi -e 's|RUNID=runXX|RUNID=run01|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
+module load ${NGS_DNA_VERSION}
+EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/
+
+perl -pi -e "s|module load ${NGS_DNA_VERSION}|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|" ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
+echo "perl -pi -e |module load ${NGS_DNA_VERSION}|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/| ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh"
 perl -pi -e 's|ngsversion=.*|ngsversion="test";\\|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
 perl -pi -e 's|create_in-house_ngs_projects_workflow.csv|create_external_samples_ngs_projects_workflow.csv|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
 perl -pi -e 's|sh \$EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh|module load Molgenis-Compute/dummy\nsh \$EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
 perl -pi -e "s|module load Molgenis-Compute/dummy|module load Molgenis-Compute/\$mcVersion|" ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
-perl -pi -e 's|WORKFLOW=\${EBROOTNGS_DNA}/workflow.csv|WORKFLOW=\${EBROOTNGS_DNA}/test_workflow.csv|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
+
+perl -pi -e 's|workflow=\${EBROOTNGS_DNA}/workflow.csv|workflow=${EBROOTNGS_DNA}/test_workflow.csv|" ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh
 cp test/PlatinumSubset.csv ${workfolder}/generatedscripts/PlatinumSubset/
 
 cd ${workfolder}/generatedscripts/PlatinumSubset/
 
-sh generate_template.sh 
+sh generate_template.sh
 
 cd scripts
-perl -pi -e 's|module load \$ngsversion|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/\n|' *.sh
+###### Load a version of molgenis compute
+perl -pi -e "s|module load test|module load ${NGS_DNA_VERSION}|
+######
+perl -pi -e "s|/apps/software/${NGS_DNA_VERSION}/|/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|g" *.sh
 sh submit.sh
 
 cd ${workfolder}/projects/PlatinumSubset/run01/jobs/
@@ -88,8 +93,8 @@ for i in $(ls s*_GenderCheck_1.sh); do touch $i.finished ; touch ${i%.*}.env; ch
 for i in $(ls s*_GenderCalculate_1.sh); do touch $i.finished ; touch ${i%.*}.env; chmod 755 ${i%.*}.env ;done
 printf "This is a male\n" > //groups/umcg-gaf//tmp04//tmp//PlatinumSubset/run01//PlatinumSample_NA12891.chosenSex.txt
 printf "Male\n" >> //groups/umcg-gaf//tmp04//tmp//PlatinumSubset/run01//PlatinumSample_NA12891.chosenSex.txt
-perl -pi -e 's|module load test|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|' s*_QCStats_*.sh  
-perl -pi -e 's|module load test|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|' s*_DecisionTree_*.sh  
+perl -pi -e 's|module load test|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|' s*_QCStats_*.sh
+perl -pi -e 's|module load test|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|' s*_DecisionTree_*.sh
 perl -pi -e 's|module load test|#|' s*_QCReport_0.sh
 perl -pi -e 's|countShScripts-3\)\)|countShScripts-4))|' s*_CountAllFinishedFiles_0.sh
 perl -pi -e 's|--time=16:00:00|--time=05:59:00|' *.sh