Merge pull request #160 from RoanKanninga/master

added GavinStandAlone + cleaning up folder

protocols/CopyResultsGavinStandAlone.sh

@@ -11,9 +11,9 @@
 #string tmpDataDir
 #string inputVcf
 
-cp ${intermediateDir}/*.GAVIN.rlv.vcf ${tmpDataDir}/GavinSA/output/
-echo "copied ${intermediateDir}/*.GAVIN.rlv.vcf ${tmpDataDir}/GavinSA/output/"
-
-name=$(basename "${inputVcf}" ".vcf")
-mv ${tmpDataDir}/GavinSA/input/${name}.{started,finished}
+cp ${intermediateDir}/*.GAVIN.rlv.vcf ${tmpDataDir}/GavinStandAlone/output/
+echo "copied ${intermediateDir}/*.GAVIN.rlv.vcf ${tmpDataDir}/GavinStandAlone/output/"
 
+name=$(basename ${inputVcf})
+mv ${tmpDataDir}/GavinStandAlone/input/${name}.{started,finished}
+mv ${tmpDataDir}/GavinStandAlone/input/processing/${name} ${tmpDataDir}/GavinStandAlone/input/done/

protocols/PrepareVcf.sh

@@ -12,11 +12,11 @@
 #list externalSampleID
 #string projectPrefix
 #list batchID
-#string inputVCF
+#string inputVcf
 
-awk '{if ($1 ~ /#/){print $0}}' "${inputVCF}" > "${intermediateDir}/header.vcf"
+awk '{if ($1 ~ /#/){print $0}}' "${inputVcf}" > "${intermediateDir}/header.vcf"
 
-awk -v var="${intermediateDir}" '{if ($1 !~ /#/){print $0 >> var"/captured.batch-"$1".vcf"}}' "${inputVCF}"
+awk -v var="${intermediateDir}" '{if ($1 !~ /#/){print $0 >> var"/captured.batch-"$1".vcf"}}' "${inputVcf}"
 
 for i in ${batchID[@]}
 do

startFromVcf.sh

@@ -3,7 +3,7 @@
 
 set -e
 set -u
-module load NGS_DNA/3.4.3-beta
+module load NGS_DNA/3.4.2
 module list
 host=$(hostname -s)
 environmentParameters="parameters_${host}"
@@ -46,7 +46,7 @@ if [[ -z "${vcfFile:-}" ]]; then echo -e '\nERROR: Must specify an inputFile (vc
 if [[ -z "${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 "${filePrefix:-}" ]]; then filePrefix=$(basename $(pwd )) ; fi ; echo "filePrefix=${filePrefix}"
+if [[ -z "${filePrefix:-}" ]]; then filePrefix=$(basename $(pwd )) ;elif [ "${filePrefix}" == "Gavin" ];then  filePrefix="Gavin_"$(basename $(pwd ));fi ; echo "filePrefix=${filePrefix}"
 if [[ -z "${runID:-}" ]]; then runID="run01" ; fi ; echo "runID=${runID}"
 
 vcfExtension=${vcfFile##*.}
@@ -118,9 +118,9 @@ ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh \
 --header "${EBROOTNGS_DNA}/templates/slurm/header.ftl" \
 --footer "${EBROOTNGS_DNA}/templates/slurm/footer.ftl" \
 --submit "${EBROOTNGS_DNA}/templates/slurm/submit.ftl" \
--w "${EBROOTNGS_DNA}/workflow_startWithVcf.csv" \
+-w "${EBROOTNGS_DNA}/workflow_startFromVcf.csv" \
 -b slurm \
 -g \
 -weave \
 -runid "${runID}" \
--o "ngsversion=${ngsversion};groupname=${group};inputVCF=${intermediateDir}/${vcfFile}"
+-o "ngsversion=${ngsversion};groupname=${group};inputVcf=${intermediateDir}/${vcfFile}"

test/test_pipeline.sh

@@ -24,7 +24,7 @@ function preparePipeline(){
 	fi
 	mkdir ${workfolder}/generatedscripts/${_projectName}/
 
-	cp ${workfolder}/tmp/NGS_DNA/generate_template.sh ${workfolder}/generatedscripts/${_projectName}/generate_template.sh
+	cp ${workfolder}/tmp/NGS_DNA/templates/generate_template.sh ${workfolder}/generatedscripts/${_projectName}/generate_template.sh
 	fgrep "computeVersion," ${workfolder}/tmp/NGS_DNA/parameters.csv > ${workfolder}/generatedscripts/${_projectName}/mcVersion.txt
 
 	module load ${NGS_DNA_VERSION}

workflow_GavinStandAlone.csv

@@ -0,0 +1,11 @@
+step,protocol,dependencies
+s01_PrepareVcf,protocols/PrepareVcf.sh,
+s02_SnpEff,protocols/SnpEff.sh,s01_PrepareVcf
+s03_CmdLineAnnotator,protocols/CmdLineAnnotator.sh,s02_SnpEff
+s04_MergeBatches,protocols/MergeBatches.sh,s03_CmdLineAnnotator;extension=annotatedExtension
+s05_SplitIndelsAndSNPs,protocols/SplitIndelsAndSNPs.sh,s04_MergeBatches
+s06a_SnpFiltration,protocols/SnpFiltration.sh,s05_SplitIndelsAndSNPs
+s06b_IndelFiltration,protocols/IndelFiltration.sh,s05_SplitIndelsAndSNPs
+s07_MergeIndelsAndSnps,protocols/MergeIndelsAndSnps.sh,s06b_IndelFiltration;s06a_SnpFiltration
+s08_Gavin,protocols/Gavin.sh,s07_MergeIndelsAndSnps
+s09_CopyGavinStandAloneResults,protocols/CopyResultsGavinStandAlone.sh,s08_Gavin