small bugfixes

parameters.csv

@@ -381,7 +381,6 @@ sampleConcordanceFile,${intermediateDir}/${externalSampleID}.ConcordanceFile.txt
 arrayTmpMap,${intermediateDir}/${externalSampleID}.concordance.tmp.map
 arrayMapFile,${intermediateDir}/${externalSampleID}.concordance.map
 familyList,${intermediateDir}/${externalSampleID}.familyList.txt
-arrayFileLocation,${inputData}/${arrayFile}
 
 mergedBamRecalibratedTable,${projectResultsDir}/alignment/${externalSampleID}.recalibrated.table
 

parameters_zinc-finger.csv

@@ -1,6 +1,6 @@
 queue,ll
-prmName,prm03
-prmHost,boxy.hpc.rug.nl
+prmName,prm05
+prmHost,coenzyme.umcg.nl
 root,/
 appsDir,${root}/apps/
 toolChain,foss-2015b

protocols/CoverageCalculations.sh

@@ -25,6 +25,9 @@ bedfileRaw=$(basename "${capturingKit}")
 if [[ "${bedfileRaw}" =~ "QXT" ]]
 then
 	bedfile=$(echo "${bedfileRaw}" | awk '{print substr($0,4)}')
+elif [[ "${bedfileRaw}" =~ "XT-HS" ]]
+then
+	bedfile=$(echo "${bedfileRaw}" | awk '{print substr($0,6)}')
 elif [[ "${bedfileRaw}" =~ "XT" ]]
 then
 	bedfile=$(echo "${bedfileRaw}" | awk '{print substr($0,3)}')

protocols/CreateInhouseProjects.sh

@@ -28,7 +28,7 @@
 #string environment_parameters
 #string ngsversion
 #string ngsUtilsVersion
-
+#string sampleSize
 #string dataDir
 
 #string coveragePerBaseDir
@@ -258,6 +258,7 @@ sh "${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh" \
 -runid "${runid}" \
 -o "ngsversion=${ngsversion};\
 batchIDList=${EBROOTNGS_DNA}/batchIDList${batching}.csv;\
+sampleSize=${sampleSize};\
 groupname=${groupname};\
 runid=${runid}"
 

protocols/VariantGenotyping.sh

@@ -17,6 +17,7 @@
 #string projectJobsDir
 #string logsDir
 #string groupname
+#string sampleSize
 
 #Function to check if array contains value
 array_contains () {
@@ -39,11 +40,10 @@ tmpProjectBatchGenotypedVariantCalls="${MC_tmpFile}"
 module load "${gatkVersion}"
 module list
 
-SAMPLESIZE=$(cat "${projectJobsDir}/${project}.csv" | wc -l)
-numberofbatches=$(("${SAMPLESIZE}" / 200))
+numberofbatches=$(("${sampleSize}" / 200))
 ALLGVCFs=()
 
-if [ "${SAMPLESIZE}" -gt 200 ]
+if [ "${sampleSize}" -gt 200 ]
 then
 	for b in $(seq 0 "${numberofbatches}")
 	do

templates/generate_template.sh

@@ -1,5 +1,13 @@
 #!/bin/bash
 
+if module list | grep -o -P 'NGS_DNA(.+)' 
+then
+	echo "DNA pipeline loaded, proceding"
+else
+	echo "No DNA Pipeline loaded, exiting"
+        exit 1
+fi
+
 module list
 
 host=$(hostname -s)
@@ -102,6 +110,7 @@ groupname=${group};\
 ngsversion=$(module list | grep -o -P 'NGS_DNA(.+)');\
 environment_parameters=${genScripts}/parameters_environment_converted.csv;\
 tmpdir_parameters=${genScripts}/parameters_tmpdir_converted.csv;\
+sampleSize=${sampleSize};\
 worksheet=${genScripts}/${filePrefix}.csv;\
 runid=${runID}" \
 -weave \

workflow.csv

@@ -31,12 +31,10 @@ s22a_MergeIndelsAndSnpsSample,protocols/MergeIndelsAndSnpsSample.sh,s21b_IndelFi
 s22b_MergeIndelsAndSnpsProject,protocols/MergeIndelsAndSnpsProject.sh,s22a_MergeIndelsAndSnpsSample
 s23_DetermineTrio,protocols/DetermineTrio.sh,s22a_MergeIndelsAndSnpsSample;s22b_MergeIndelsAndSnpsProject
 s24a_Gavin,protocols/Gavin.sh,s22a_MergeIndelsAndSnpsSample;s22b_MergeIndelsAndSnpsProject
-s24b_CartegeniaTree,protocols/CartegeniaTree.sh,s24a_Gavin
-s24c_CartegeniaFiltering,protocols/CartegeniaFiltering.sh,s24b_CartegeniaTree
 s25a_CompressingSampleVcf,protocols/CompressingFinalVcf.sh,s22a_MergeIndelsAndSnpsSample;s22b_MergeIndelsAndSnpsProject;finalVcf=sampleFinalVcf
 s25b_CompressingProjectVcf,protocols/CompressingFinalVcf.sh,s22a_MergeIndelsAndSnpsSample;s22b_MergeIndelsAndSnpsProject;finalVcf=projectFinalVcf
 s26_VcfToTable,protocols/VcfToTable.sh,s22a_MergeIndelsAndSnpsSample;s22b_MergeIndelsAndSnpsProject
 s27_InSilicoConcordance,protocols/InSilicoConcordance.sh,s26_VcfToTable
 s28_MultiQC,protocols/MultiQC.sh,s08a_CollectMultipleMetrics;s08b_CollectHSMetrics;s08d_CollectGCBiasMetrics;s08c_CollectBamIndexMetrics;s10_Flagstat;s27_InSilicoConcordance
-s29_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s11_Manta;s12c_DecisionTree;s13_CramConversion;s14_MakeDedupBamMd5;s23_DetermineTrio;s24c_CartegeniaFiltering;s25a_CompressingSampleVcf;s25b_CompressingProjectVcf;s15_CoverageCalculations;s28_MultiQC
+s29_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s11_Manta;s12c_DecisionTree;s13_CramConversion;s14_MakeDedupBamMd5;s23_DetermineTrio;s24a_Gavin;s25a_CompressingSampleVcf;s25b_CompressingProjectVcf;s15_CoverageCalculations;s28_MultiQC
 s30_CopyToResultsDir,protocols/CopyToResultsDir.sh,s29_CountAllFinishedFiles