parameters_gearshift.csv

#Tools
pythonVersion,PythonPlus/3.7.4-foss-2018b-v20.11.1
pythonEnvironment,/groups/umcg-wijmenga/tmp01/projects/pgx-pipeline/tools/virtualenv/3.7.4-foss-2018b-v20.11.1
computeVersion,Molgenis-Compute/v19.01.1-Java-11-LTS
#pennCNVVersion,PennCNV/1.0.4-foss-2018b
optiCallExecutable,/groups/umcg-wijmenga/tmp01/projects/pgx-pipeline/tools/tss101-opticall-090d8ed4136a/opticall/opticall
RPlusVersion,RPlus/4.0.3-foss-2018b-v21.01.1
plinkVersion,PLINK/1.9-beta6-20190617
htslibVersion,HTSlib/1.11-GCCcore-7.3.0
boostVersion,Boost/1.67.0-foss-2018b
shapeitExecutable,/groups/umcg-wijmenga/tmp01/projects/pgx-pipeline/tools/shapeit4-4.2.1/bin/shapeit4.2

#zCallVersion,opticall/0.7.0-foss-2015b
#GTCtoVCFVersion,GTCtoVCF/1.1.1-foss-2015b-Python-2.7.11

#references
bpmFileVersion1,/apps/data/GSAarray/GSAMD-24v1-0_20011747_A5.bpm
bpmFileVersion3,/apps/data/GSAarray/GSAMD-24v3-0-EA_20034606_A1.bpm
#hmmFile,hhall.hmm # TODO: remove?
#pfbFile,/apps/data/GSAarray/GSA-MD_pfb.pfb # TODO: remove?
MAFref,/groups/umcg-wijmenga/tmp04/umcg-raguirre/pln_ugli/af.ref.data.txt
ref1000G,/apps/data/1000G/phase3
pops1000G,/apps/data/1000G/populationInfo/20130606_sample_info_pop_superpop.xlsx
gonlref,/groups/umcg-aad/tmp04/umcg-elopera/thgref
variantsPassedValidation,/groups/umcg-wijmenga/tmp01/projects/pgx-pipeline/data/passport_generation

#paths
root,/
appsDir,${root}/apps/
workDir,/groups/${group}/
tmpDir,${workDir}/${tmpName}/
tmpTmpdir,${tmpDir}/tmp/
intermediateDir,${tmpTmpdir}/${Project}/${runid}/
projectDir,${workDir}/${tmpName}/projects/
resultDir,${projectDir}/${Project}/${runid}/results/
projectJobsDir,${projectDir}/${Project}/${runid}/jobs/
genScripts,${tmpDir}/generatedscripts/${Project}
diagnosticOutputFolder,${tmpDir}/DiagnosticOutput
projectRawTmpDataDir,${projectDir}/${Project}/${runid}/rawdata/array/
IDATprmDataDir,${workDir}/${prmName}/rawdata/array/IDAT/
GTCprmDataDir,${workDir}/${prmName}/rawdata/array/GTC/
IDATtmpDataDir,${workDir}/${tmpName}/rawdata/array/IDAT/
GTCtmpDataDir,${workDir}/${tmpName}/rawdata/array/GTC/
ateambotUser,${group}-ateambot
logsDir,${workDir}/${tmpName}/logs/
concordanceInputDir,/groups/umcg-gd/${tmpName}/Concordance/array/
arrayFinalReport,${intermediateDir}/${Project}_${SentrixBarcode_A}_finalreport.txt
optiCallDir,${resultDir}/opticall
zCallDir,${intermediateDir}/zCall
pennCNVInputDir,${resultDir}/PennCNV/inputfiles/
pennCNVDir,${resultDir}/PennCNV/
CallrateDir,${intermediateDir}/Callrate/
genSampleDir,${resultDir}/gensamplefiles
AutosomeQCDir,${resultDir}/GeneralQC
output80,${AutosomeQCDir}/1_CR80
CR_high,${AutosomeQCDir}/2_CR_high
outputMH,${AutosomeQCDir}/3_MAF_HWE
Het,${AutosomeQCDir}/4_Het
Relatedness,${AutosomeQCDir}/5_Relatedness
repout,${AutosomeQCDir}/plots
PCA,${AutosomeQCDir}/6_PCA
X_QCDir,${AutosomeQCDir}/X_QC_sexcheck
X_output80,${X_QCDir}/1_CR80
X_CR_high,${X_QCDir}/2_CR_high
X_outputMH,${X_QCDir}/3_MAF_HWE
X_repout,${X_QCDir}/plots