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Commit e214a50d authored by Hanna  JULIENNE's avatar Hanna JULIENNE
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resolve conflict in pipeline

parent b6acf71b
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1 merge request!2Pipeline ancestry
......@@ -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
......
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