parameters_pgx_pipeline_2022-10-31.csv

#Tools
molgenisStandInScript,/groups/umcg-fg/tmp01/projects/pgx-passport/tools/PGx-pipeline/molgenis_stand_in_script.sh
pythonVersion,Python/3.9.1-GCCcore-7.3.0-bare
pythonEnvironment,/groups/umcg-fg/tmp01/projects/pgx-passport/tools/virtualenv/3.9.1-GCCcore-7.3.0-bare
#computeVersion,Molgenis-Compute/v19.01.1-Java-11-LTS
#pennCNVVersion,PennCNV/1.0.4-foss-2018b
optiCallExecutable,/groups/umcg-fg/tmp01/projects/pgx-passport/tools/tss101-opticall-090d8ed4136a/opticall/opticall
RPlusVersion,RPlus/4.0.3-foss-2018b-v21.01.1
plinkVersion,PLINK/1.9-beta6-20190617
plink2Version,PLINK/2.0-alpha2-20191006
htslibVersion,HTSlib/1.11-GCCcore-7.3.0
bcftoolsVersion,BCFtools/1.16-GCCcore-11.3.0
boostVersion,Boost/1.67.0-foss-2018b
shapeitExecutable,/groups/umcg-fg/tmp01/projects/pgx-passport/tools/shapeit4-4.2.1/bin/shapeit4.2

#References
variantsPassedValidation,/groups/umcg-fg/tmp01/projects/pgx-passport/data/passport_generation

#Imputation pipeline
javaVersion,Java/11-LTS
nextflowPath,/groups/umcg-fg/tmp01/projects/pgx-passport/tools/nextflow
imputationPipelineReferencePath,/groups/umcg-fg/tmp01/projects/pgx-passport/data/processed/imputationreference/
outputName,genimpute_phased_imputed

#Settings
imputationFlankSize,1000000