diff --git a/jass_pipeline.nf b/jass_pipeline.nf index c6d5106135b5c4007cd58505519b5c558d6bdbb8..816d7b80c23964e62f2454f61861265e8f4878ea 100644 --- a/jass_pipeline.nf +++ b/jass_pipeline.nf @@ -16,13 +16,9 @@ params.meta_data = "${projectDir}"+"/input_files/Data_test_EAS.csv" // file desc params.gwas_folder = "${projectDir}"+'/test_data/hg38_EAS/' params.ref_panel = '/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/Ref_panel_by_chr/' params.region = "${projectDir}"+"/input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed" -<<<<<<< HEAD -param.ref_panel_wg_channel = "${projectDir}"+"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv" -======= params.ref_panel_WG = "${projectDir}"+"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv"//"${projectDir}/Ref_Panel/1000G_EAS_0_01_chr22.csv" ->>>>>>> 1e9f87b9950df3c765cf738e14fac767e4ecba8a params.ancestry="EAS" params.prefix="ALL_ensemble_1000G_hg38_EAS_chr" params.prefix_Impute_GWAS="ALL_ensemble_1000G_hg38_EAS_" @@ -58,10 +54,6 @@ chr_channel = Channel.from(1..22) ref_chr_channel=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim") ld_channel=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Matrix_LD_RAISS/EAS/*.ld") -<<<<<<< HEAD -//"${projectDir}/Ref_Panel/1000G_EAS_0_01_chr22.csv" -======= ->>>>>>> 1e9f87b9950df3c765cf738e14fac767e4ecba8a extract_sample_size_script_channel = Channel.fromPath("${projectDir}/bin/extract_sample_size.py") generate_trait_pairs_channel = Channel.fromPath("${projectDir}/bin/generate_trait_pairs.py") parse_correlation_channel = Channel.fromPath("${projectDir}/bin/parse_correlation_results.py") @@ -86,11 +78,7 @@ process Clean_GWAS { publishDir "${params.output_folder}/harmonized_GWAS_files/", pattern: "*.txt", mode: 'copy' publishDir "${params.output_folder}", pattern: "harmonized_GWAS_1_file/*.txt", mode: 'copy' input: -<<<<<<< HEAD - path ref_panel from params.ref_panel_wg_channel -======= path ref_panel from params.ref_panel_WG ->>>>>>> 1e9f87b9950df3c765cf738e14fac767e4ecba8a path meta_chunk from meta_data output: path "harmonized_GWAS_1_file/*.txt" into cleaned_gwas_channel