parameters.csv

# Defaults
dataDir,/apps/data/
pgxDataDir,${dataDir}/PGx/
optiCallVersion,opticall/0.8.1-${toolChain_min}
plinkVersion,PLINK/1.9-beta6-20190617
plink2Version,PLINK/2.0-alpha4.5-20230813
shapeItVersion,SHAPEIT4/4.2.2-${toolChain_max}
asterixVersion,asterix/1.0
computeVersion,20.03.1-Java-11-LTS
gapVersion,GAP/2.8.0
pythonVersion,Python/3.9.1-${toolChain_min}-bare
boostVersion,Boost/1.79.0-GCC-11.3.0
htslibVersion,HTSlib/1.19.1-${toolChain_min}
rVersion,R/4.2.2-foss-2022a
nextflowVersion,nextflow/21.10.6-Java-11-LTS
bcfToolsVersion,BCFtools/1.19-${toolChain_min}
javaVersion,Java/11-LTS
ngsUtilsVersion,ngs-utils/24.03.1

pythonEnvironment,/groups/umcg-pgx/tmp07/pythonVirtualEnv/

variantsPassedQualityControl,${pgxDataDir}/GSAMD-24v3/passed_variants_qc.txt
imputationPipelineReferencePath,${pgxDataDir}/processed/imputationreference
bpmFile,${dataDir}/GSAarray/GSAMD-24v3-0-EA_20034606_A1.bpm
cnvConfig,${pgxDataDir}/cyp2d6/config.yml
cnvBedFile,${pgxDataDir}/cyp2d6/cyp2d6.bed
pgxGenesBed37,${pgxDataDir}/pgx-genes_GRCh37.bed
pgxGenesBed38,${pgxDataDir}/pgx-genes_GRCh38.bed
pgxGenesBed38Flanked,${pgxDataDir}/pgx-genes_GRCh38_1Mb-flanks.bed
gnomadAnnotationFile,${pgxDataDir}/gnomad/analyses/concatenated_pgx_genes/out/pgx_genes_gnomad_chromosomes_renamed.vcf.gz
correctiveVariantsOutputDir,${pgxDataDir}/analyses/select_corrective_variants/out
asterixDefaultJson,${pgxDataDir}/analyses/asterix/hl7_asterix_default.json
translationTableHaploToCiDir,${pgxDataDir}/analyses/translation_tables/MDv3/haplo_to_ci/20240611/
translationTableSnpToHaploDir,${pgxDataDir}/analyses/translation_tables/MDv3/snp_to_haplo/20240611/
outputName,genimpute_phased_imputed
imputationFlankSize,1000000
cnvBatchCorrectionPath,${pgxDataDir}/analyses/cyp2d6_cnv_calling/20240730/out
tmpDataDir,${groupDir}/${tmpName}/
projectDir,${tmpDataDir}/projects/${project}/
projectJobsDir,${projectDir}/jobs/
intermediateDir,${tmpDataDir}/tmp/${project}/
rawdataPath,${tmpDataDir}/rawdata/
outdir,${intermediateDir}/analyses/
resultsDir,${projectDir}/results/
finalReportsDir,${outdir}/final_reports/
finalReportTxt,${finalReportsDir}/${SentrixBarcode_A}_finalreport.txt
finalReport,${finalReportsDir}/${SentrixBarcode_A}_finalreport.txt.gz
genotypesOxfordPrefix,${gtcDataDir}/results/oxford_gen_sample/chr_${chr}
genotypesPlinkPrefix,${outdir}/qced_plink_files/chr_${chr}
sampleListPrefix,${outdir}/quality_controlled_samples/sample_list
concatenatedGenotypesOutputDir,${outdir}/concatenated_genotypes/
stagedIntensitiesDir,${outdir}/staged_intensities/
stagedIntensities,${stagedIntensitiesDir}/${SentrixBarcode_A}_intensities.pkl
cnvOutDir,${outdir}/cyp2d6_cnv_calling/out
gtcDataDir,${rawdataPath}/hematologie_research_data/${project}/
imputationOutputDir,${outdir}/impute_pgx_genes/
asterixOutputDir,${resultsDir}/asterix/