diff --git a/jass_pipeline.nf b/jass_pipeline.nf index 06dd01df532648eb1510a7c3090487d2cc00c64e..e1c5a7c95c3f80d1f55ee8e40df655e8b0dc9006 100644 --- a/jass_pipeline.nf +++ b/jass_pipeline.nf @@ -16,12 +16,12 @@ params.meta_data = "${projectDir}"+"/input_files/Data_test_EAS.csv" // "${projectDir}"+"/input_files/Meta_data_preliminary_analysis.csv" file describing gwas summary statistic format params.gwas_folder = "${projectDir}"+'/test_data/hg38_EAS/' -params.region = Channel.fromPath("${projectDir}"+"/input_files/All_Regions_ALL_ensemble_1000G_hg38_EUR.bed") +params.region = Channel.fromPath("${projectDir}"+"/input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed") params.ref_panel_WG = "${projectDir}"+"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv" params.ancestry="EAS" -params.prefix="ALL_ensemble_1000G_hg38_EUR_chr" +params.prefix="ALL_ensemble_1000G_hg38_EAS_chr" params.prefix_Impute_GWAS="ALL_ensemble_1000G_hg38_EAS_" params.suffix="" params.LD_SCORE_folder='/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Matrix_LDSCORE/EAS/' @@ -45,7 +45,7 @@ params.ld_type = "plink" params.ld_folder = Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Matrix_LD_RAISS/EAS/*.ld").collect() params.ref_panel = '/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/Ref_panel_by_chr/' chr_channel = Channel.from(1..22) -params.ref_chr_path= Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/EUR/ALL_ensemble_1000G_hg38_EUR_chr*.bim").collect() +params.ref_chr_path= Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/EAS/ALL_ensemble_1000G_hg38_EAS_chr*.bim").collect() params.perform_sanity_checks=false params.perform_accuracy_checks=false