changed gitattributes

.gitattributes

@@ -1 +0,0 @@
-* text eol=lf

modules/compute/protocols/imputation/impute2/calculateBeagleR2ForImpute2Results.ftl

@@ -1,18 +1,12 @@
 #MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4
 
-#EXES calculateBeagleR2ForIMpute2ResultsPythonScript
-#LOGS log
-
 #FOREACH project,chr
 
+getFile ${calculateBeagleR2ForIMpute2ResultsPythonScript}
 
-for file in $(ls ${imputationResultDir}/chr_${chr})
-do
-	getFile $file;
-done
-putFile "${imputationResultDir}/chr_${chr}.beagleR2"
+getFile ${imputationResultDir}/chr_${chr}
+putFile ${imputationResultDir}/chr_${chr}.beagleR2
 
-getFile ${calculateBeagleR2ForIMpute2ResultsPythonScript}
 
 inputs "${imputationResultDir}/chr_${chr}"
 alloutputsexist "${imputationResultDir}/chr_${chr}.beagleR2"

modules/compute/protocols/imputation/impute2/concatImpute2ResultsPerChr.ftl

@@ -3,19 +3,19 @@
 #FOREACH project,chr
 
 <#list impute2ResultChrBinInfoFile as infoFile>
-	getFile ${infoFile}
+	getFile "${infoFile}"
 </#list>
 <#list impute2ResultChrBinGenFile as genFile>
-	getFile ${genFile}
+	getFile "${genFile}"
 </#list>
-putFile ${imputationResultDir}/chr_${chr}
-putFile ${imputationResultDir}/chr_${chr}_info
+putFile "${imputationResultDir}/chr_${chr}"
+putFile "${imputationResultDir}/chr_${chr}_info"
 
 
-inputs ${ssvQuoted(impute2ResultChrBinInfoFile)}
-inputs ${ssvQuoted(impute2ResultChrBinGenFile)}
-alloutputsexist ${imputationResultDir}/chr_${chr}
-alloutputsexist ${imputationResultDir}/chr_${chr}_info
+inputs "${ssvQuoted(impute2ResultChrBinInfoFile)}"
+inputs "${ssvQuoted(impute2ResultChrBinGenFile)}"
+alloutputsexist "${imputationResultDir}/chr_${chr}"
+alloutputsexist "${imputationResultDir}/chr_${chr}_info"
 
 #Concat the bins with compute for each
 

modules/compute/protocols/imputation/impute2/convertConcatedImpute2ResultToPedMap.ftl

@@ -1,8 +1,5 @@
 #MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4
 
-#EXES gtoolBin
-#LOGS log
-
 #FOREACH project,chr
 
 getFile "${imputationResultDir}/chr_${chr}"

modules/compute/protocols/imputation/impute2/convertPedMapToTriTyper.ftl

@@ -1,13 +1,11 @@
 #MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4
 
-
-#INPUTS studyPedMap.map,studyPedMap.ped
-#OUTPUTS studyTriTyperChrDir
-#EXES imputationToolJar
-#LOGS log
-
 #FOREACH project,chr
 
+getFile "${imputationToolJar}"
+getFile "${imputationToolJsciCoreJar}"
+getFile "${imputationToolGeneticaLibraries}"
+
 getFile "${studyPedMapChr}.map"
 getFile "${studyPedMapChr}.ped"
 putFile "${studyTriTyperChrDir}/GenotypeMatrix.dat"
@@ -28,11 +26,12 @@ alloutputsexist "${studyTriTyperChrDir}/SNPsHash.txt"
 alloutputsexist "${studyTriTyperChrDir}/SNPs.txt"
 
 
-#module load ${imputationToolJar}/${imputationToolJarversion}
-
 mkdir -p ${studyTriTyperChrTempDir}
 
-java -jar ${imputationToolJar} --mode pmtt --in ${studyPedMapChrDir} --out ${studyTriTyperChrTempDir}
+java -jar ${imputationToolJar} \
+--mode pmtt \
+--in ${studyPedMapChrDir} \
+--out ${studyTriTyperChrTempDir}
 
 
 #Get return code from last program call

modules/compute/protocols/imputation/impute2/parameters.csv

@@ -38,7 +38,10 @@ referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash
 impute2Bin,${tooldir}/impute_${impute2Binversion}/impute2,,,
 impute2Binversion,v2.2.2_x86_64_static,,,
 imputationToolJar,${tooldir}/ImputationTool-${imputationToolJarversion}/ImputationTool.jar,,,
-imputationToolJarversion,20120912,,,
+imputationToolJarversion,20120912,,,
+imputationToolLibDir,${tooldir}/ImputationTool-${imputationToolJarversion}/lib/,,,
+imputationToolGeneticaLibrariesjar,${imputationToolLibDir}/GeneticaLibraries.jar,,,
+imputationToolJsciCoreJar,${imputationToolLibDir}/jsci-core-1.1.jar,,,
 referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.impute.hap,,,
 referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.impute.legend,,,
 referenceImpute2MapFile,${referenceImpute2Dir}/genetic_map_chr${chr}_combined_b37.txt,,,

modules/compute/protocols/imputation/impute2/preparePedMapForImpute2.ftl

@@ -1,15 +1,11 @@
 #MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4
 
-
-#EXES
-#LOGS log
-
 #FOREACH project,chr
 
-getFile "${studyInputPedMapChr}.map"
-getFile "${studyInputPedMapChr}.ped"
-putFile "${studyPedMapChr}.map"
-putFile "${studyPedMapChr}.ped"
+getFile ${studyInputPedMapChr}.map
+getFile ${studyInputPedMapChr}.ped
+putFile ${studyPedMapChr}.map
+putFile ${studyPedMapChr}.ped
 
 
 inputs "${studyInputPedMapChr}.map"
@@ -26,4 +22,3 @@ awk '{$2=$1"_"$4; print $0}' ${studyInputPedMapChr}.map > ${studyPedMapChr}.map
 cp ${studyInputPedMapChr}.ped ${studyPedMapChr}.ped
 
 #Becarefull of phenotype field in ped files. Might crash later on -9
-

modules/compute/protocols/imputation/impute2/prepareStudy.ftl

@@ -1,12 +1,10 @@
 #MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=8
 
-#INPUTS studyTriTyperChrDir,referenceTriTyperDir
-#OUTPUTS preparedStudyDir
-#EXES imputationToolJar
-#LOGS log
-
 #FOREACH project,chr
 
+getFile "${imputationToolJar}"
+getFile "${imputationToolJsciCoreJar}"
+getFile "${imputationToolGeneticaLibraries}"
 
 getFile ${studyTriTyperChrDir}/GenotypeMatrix.dat
 getFile ${studyTriTyperChrDir}/Individuals.txt
@@ -18,26 +16,31 @@ getFile ${referenceTriTyperDir}/Individuals.txt
 getFile ${referenceTriTyperDir}/PhenotypeInformation.txt
 getFile ${referenceTriTyperDir}/SNPMappings.txt
 getFile ${referenceTriTyperDir}/SNPs.txt
-
-for file in $(ls ${preparedStudyTempDir})
-do
-putFile $file;
-done
-
+putFile ${preparedStudyDir}/chr${chr}.dat
+putFile ${preparedStudyDir}/chr${chr}.gen
+putFile ${preparedStudyDir}/chr${chr}.map
+putFile ${preparedStudyDir}/chr${chr}.markersbeagleformat
+putFile ${preparedStudyDir}/chr${chr}.ped
+putFile ${preparedStudyDir}/chr${chr}.sample
+putFile ${preparedStudyDir}/exportlog.txt
 
-inputs ${studyTriTyperChrDir}/GenotypeMatrix.dat
-inputs ${studyTriTyperChrDir}/Individuals.txt
-inputs ${studyTriTyperChrDir}/PhenotypeInformation.txt
-inputs ${studyTriTyperChrDir}/SNPMappings.txt
-inputs ${studyTriTyperChrDir}/SNPs.txt
-inputs ${referenceTriTyperDir}/GenotypeMatrix.dat
-inputs ${referenceTriTyperDir}/Individuals.txt
-inputs ${referenceTriTyperDir}/PhenotypeInformation.txt
-inputs ${referenceTriTyperDir}/SNPMappings.txt
-inputs ${referenceTriTyperDir}/SNPs.txt
-
-
-#module load ${imputationToolJar}/${imputationToolJarversion}
+inputs "${studyTriTyperChrDir}/GenotypeMatrix.dat"
+inputs "${studyTriTyperChrDir}/Individuals.txt"
+inputs "${studyTriTyperChrDir}/PhenotypeInformation.txt"
+inputs "${studyTriTyperChrDir}/SNPMappings.txt"
+inputs "${studyTriTyperChrDir}/SNPs.txt"
+inputs "${referenceTriTyperDir}/GenotypeMatrix.dat"
+inputs "${referenceTriTyperDir}/Individuals.txt"
+inputs "${referenceTriTyperDir}/PhenotypeInformation.txt"
+inputs "${referenceTriTyperDir}/SNPMappings.txt"
+inputs "${referenceTriTyperDir}/SNPs.txt"
+alloutputsexist "${preparedStudyDir}/chr${chr}.dat"
+alloutputsexist "${preparedStudyDir}/chr${chr}.gen"
+alloutputsexist "${preparedStudyDir}/chr${chr}.map"
+alloutputsexist "${preparedStudyDir}/chr${chr}.markersbeagleformat"
+alloutputsexist "${preparedStudyDir}/chr${chr}.ped"
+alloutputsexist "${preparedStudyDir}/chr${chr}.sample"
+alloutputsexist "${preparedStudyDir}/exportlog.txt"
 
 mkdir ${preparedStudyTempDir}