diff --git a/README.md b/README.md
index 1a7de06c..7155bf42 100755
--- a/README.md
+++ b/README.md
@@ -26,3 +26,4 @@ A joint analysis has been performed of all the samples in the project. This lead
 <a name="r4"> 4. McKenna et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. </a>
 
 <a name="r5"> 5. Van der Auwera et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.</a>
+
diff --git a/docs/ngs-quickstart.md b/docs/ngs-quickstart.md
index 93a0f664..8a64edb7 100644
--- a/docs/ngs-quickstart.md
+++ b/docs/ngs-quickstart.md
@@ -5,7 +5,7 @@ This is the Quick tutorial, when there are problems first go to the detailed [in
 We first have to load EasyBuild, this can be done with this command
 ```bash
 module load EasyBuild
-eb NGS_DNA-3.4.3.eb --robot -–robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
+eb NGS_DNA-3.4.4.eb --robot -–robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
 ```
 **_Note:_** some software cannot be downloaded automagically due to for example licensing or technical issues and the build will fail initially.
 In these cases you will have to download manually and copy the sources to
diff --git a/startFromVcf.sh b/startFromVcf.sh
index 52c5fb8b..37a8ddd9 100755
--- a/startFromVcf.sh
+++ b/startFromVcf.sh
@@ -1,9 +1,8 @@
 #!/bin/bash
 
-
 set -e
 set -u
-module load NGS_DNA/3.4.3
+module load NGS_DNA/3.4.4
 module list
 host=$(hostname -s)
 environmentParameters="parameters_${host}"
diff --git a/templates/generate_template.sh b/templates/generate_template.sh
index d47ace12..921db029 100755
--- a/templates/generate_template.sh
+++ b/templates/generate_template.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-module load NGS_DNA/3.4.3
+module load NGS_DNA/3.4.4
 module list
 host=$(hostname -s)
 environmentParameters="parameters_${host}"
diff --git a/templates/generate_template_gonl.sh b/templates/generate_template_gonl.sh
deleted file mode 100755
index e9779196..00000000
--- a/templates/generate_template_gonl.sh
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/bin/bash
-
-module load NGS_DNA/3.4.0
-module list 
-HOST=$(hostname)
-thisDir=$(pwd)
-
-ENVIRONMENT_PARAMETERS="parameters_${HOST%%.*}.csv"
-TMPDIRECTORY=$(basename $(cd ../../ && pwd ))
-GROUP=$(basename $(cd ../../../ && pwd ))
-
-PROJECT=projectXX
-WORKDIR="/groups/${GROUP}/${TMPDIRECTORY}"
-RUNID=runXX
-
-## Normal user, please leave BATCH at _chr
-## For expert modus: small batchsize (6) fill in '_small'  or per chromosome fill in _chr
-BATCH="_b38_chr"
-samplesheet=${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv
-mac2unix $samplesheet
-
-python ${EBROOTNGS_DNA}/scripts/samplesize.py ${samplesheet} $thisDir
-SAMPLESIZE=$(cat externalSampleIDs.txt | uniq | wc -l)
-
-python ${EBROOTNGS_DNA}/scripts/gender.py $samplesheet
-var=$(cat ${samplesheet}.tmp | wc -l)
-
-if [ $var != 0 ]
-then
-    	mv ${samplesheet}.tmp ${samplesheet}
-        echo "samplesheet updated with Gender column"
-fi
-echo "Samplesize is $SAMPLESIZE"
-
-if [ $SAMPLESIZE -gt 199 ]
-then
-    	WORKFLOW=${EBROOTNGS_DNA}/workflow_samplesize_bigger_than_200.csv
-else
-        WORKFLOW=${EBROOTNGS_DNA}/workflow_gonl.csv
-fi
-
-if [ -f .compute.properties ];
-then
-     rm .compute.properties
-fi
-
-if [ -f ${WORKDIR}/generatedscripts/${PROJECT}/out.csv ];
-then
-    	rm -rf ${WORKDIR}/generatedscripts/${PROJECT}/out.csv
-fi
-
-echo "tmpName,${TMPDIRECTORY}" > ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters.csv 
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters.csv > \
-${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters_gonl.csv > \
-${WORKDIR}/generatedscripts/${PROJECT}/out.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters_${GROUP}.csv > \
-${WORKDIR}/generatedscripts/${PROJECT}/group_parameters.csv
-
-perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/${ENVIRONMENT_PARAMETERS} > \
-${WORKDIR}/generatedscripts/${PROJECT}/environment_parameters.csv
-
-sh $EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh \
--p ${WORKDIR}/generatedscripts/${PROJECT}/out.csv \
--p ${WORKDIR}/generatedscripts/${PROJECT}/group_parameters.csv \
--p ${WORKDIR}/generatedscripts/${PROJECT}/environment_parameters.csv \
--p ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv \
--p ${EBROOTNGS_DNA}/batchIDList${BATCH}.csv \
--p ${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv \
--w ${EBROOTNGS_DNA}/create_external_samples_ngs_projects_workflow.csv \
--rundir ${WORKDIR}/generatedscripts/${PROJECT}/scripts \
---runid ${RUNID} \
--o "workflowpath=${WORKFLOW};\
-outputdir=scripts/jobs;mainParameters=${WORKDIR}/generatedscripts/${PROJECT}/out.csv;\
-group_parameters=${WORKDIR}/generatedscripts/${PROJECT}/group_parameters.csv;\
-groupname=${GROUP};\
-ngsversion=$(module list | grep -o -P 'NGS_DNA(.+)');\
-environment_parameters=${WORKDIR}/generatedscripts/${PROJECT}/environment_parameters.csv;\
-tmpdir_parameters=${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv;\
-batchIDList=${EBROOTNGS_DNA}/batchIDList${BATCH}.csv;\
-worksheet=${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv" \
--weave \
---generate
-
diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
index fd64e03a..48668d2e 100644
--- a/test/test_pipeline.sh
+++ b/test/test_pipeline.sh
@@ -131,7 +131,7 @@ fi
 echo "pr number: $1"
 
 PULLREQUEST=$1
-NGS_DNA_VERSION=NGS_DNA/3.4.3
+NGS_DNA_VERSION=NGS_DNA/3.4.4
 
 git clone https://github.com/molgenis/NGS_DNA.git
 cd ${workfolder}/tmp/NGS_DNA