diff --git a/Ref_Panel/1000G_AFR_0_01.csv b/Ref_Panel/1000G_AFR_0_01.csv
new file mode 100755
index 0000000000000000000000000000000000000000..34732ab61353114c4ab406dce02a6e50b3520077
--- /dev/null
+++ b/Ref_Panel/1000G_AFR_0_01.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:934c63984d760943b0228802f1fcbf3a778d8a3c525e3b78138948b4c07f4ab4
+size 515852597
diff --git a/Ref_Panel/1000G_EAS_0_01.csv b/Ref_Panel/1000G_EAS_0_01.csv
new file mode 100755
index 0000000000000000000000000000000000000000..83ab685c2be8a4bd213ad117ab991b01600d6f0a
--- /dev/null
+++ b/Ref_Panel/1000G_EAS_0_01.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:254d08862169ae17658e38094ee8bddbe01571a4e56b9058713abc8b706f8081
+size 262350635
diff --git a/modules/GW_reference_panels.nf b/modules/GW_reference_panels.nf
new file mode 100644
index 0000000000000000000000000000000000000000..6e02d7c7628d0f3eb4ef21bbed68c691d3d5aeb2
--- /dev/null
+++ b/modules/GW_reference_panels.nf
@@ -0,0 +1,82 @@
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ JASS suite pipeline
+authors : Hanna Julienne, Hervé Ménager & Lucie Troubat
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+/* Parameter to set if optional pipeline steps are performed */
+params.compute_project=false
+
+
+/* path of input data */
+params.ref_panel = '/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/EAS/'
+
+params.region = '/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Regions_LD/EAS/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed'
+params.output_folder = "${launchDir}"
+
+params.ancestry="EAS"
+params.prefix="ALL_ensemble_1000G_hg38_EAS_chr"
+params.prefix_Impute_GWAS="ALL_ensemble_1000G_hg38_EAS_"
+params.suffix=""
+
+
+chr_channel = Channel.from(1..22)
+
+ref_chr_channel=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim")
+ref_chr_channel2=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim")
+ref_chr_channel3=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.*")
+
+
+process Compute_MAF{
+
+ input:
+ file ref_panel from ref_chr_channel3.collect()
+ val chr from chr_channel
+ output:
+ file "*.frq" into MAF_channel
+ """
+ echo "Compute_MAF"
+
+ bfile="${params.prefix}${chr}${params.suffix}"
+ echo \$bfile
+
+ plink --bfile \${bfile} --freq --out ./chr${chr}
+
+ """
+}
+
+process create_WG_reference_panel{
+ publishDir "${launchDir}/Ref_Panel", pattern: "*.csv", mode: 'copy'
+
+ input:
+ file maf_files from MAF_channel.collect()
+ file chr_files from ref_chr_channel.collect()
+ output:
+ file "1000G_${params.ancestry}_0_01.csv" into ref_panel_wg_channel
+ """
+ #!/usr/bin/env python3
+ import subprocess as sub
+ import pandas as pd
+ import os
+ cwd = os.getcwd()
+ print(cwd)
+ pref="${params.prefix}"
+ suf="${params.suffix}"
+ refchr_list = []
+ for chrom in range(1,23):
+ fi = "{0}{1}{2}.bim".format(pref,chrom,suf)
+ print(fi)
+ print(type(fi))
+ position = pd.read_csv(fi, sep='\t', names=['chr', "rsid", "?", "pos", "ref_al", "alt_al"])
+ position.set_index("rsid", inplace=True)
+ ref_chr = pd.read_csv("./chr{0}.frq".format(chrom), sep="\\s+")
+
+ ref_chr['pos'] = position.loc[ref_chr.SNP, "pos"].values
+ refchr_list.append(ref_chr[["CHR", "pos", "SNP", "A1", "A2", "MAF"]])
+
+ ref= pd.concat(refchr_list)
+ ref.loc[~(ref.A1+ref.A2).isin(["AT", 'TA','CG','GC'])][["CHR","SNP", "MAF", "pos", "A1", "A2"]].to_csv("1000G_${params.ancestry}_0_01.csv", index=False, header=False, sep="\t")
+ """
+}
diff --git a/modules/run_RAISS_perf.nf b/modules/run_RAISS_perf.nf
new file mode 100755
index 0000000000000000000000000000000000000000..61b6a3f592a2ee5758e16ce68f8c8c459419c7ee
--- /dev/null
+++ b/modules/run_RAISS_perf.nf
@@ -0,0 +1,34 @@
+
+params.ref_panel = '/pasteur/zeus/projets/p02/GGS_WKD/DATA_GnomAD/hg37/FINNS/ref_panel'
+params.output_folder = "/pasteur/zeus/projets/p02/GGS_JASS/DATA_BATCH_04_11_2022/"
+ref_chr_channel2=Channel.fromPath(params.ref_panel+"/chr*.bim")
+
+ld_channel=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_GnomAD/hg37/FINNS/ld_mat/*")
+cleaned_gwas_chr_channel = Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/DATA_BATCH_04_11_2022/harmonized_new_index/z_*chr22.txt")
+
+
+
+process perf_raiss {
+ publishDir "${params.output_folder}", pattern: "imputed_gnomad/*.txt", mode: 'copy'
+
+ input:
+ file gwas_files from cleaned_gwas_chr_channel
+ file ref_file from ref_chr_channel2.collect()
+ file ld_file from ld_channel.collect()
+ output:
+ file "imputed_gnomad/*.txt" into imputed_gwas_channel
+ script:
+ """
+ mkdir -p imputed_gnomad
+ mkdir -p masked_zscore
+ mkdir -p raiss_report
+ chrom=\$(echo ${gwas_files} | cut -d '_' -f4 | cut -d "." -f1)
+ study=\$(echo ${gwas_files} | cut -d '_' -f2,3)
+
+ echo \$chrom
+ echo \$study
+
+ raiss --ld-folder ./ --ref-folder ./ --gwas \$study --chrom chr22 --ld-type scipy performance-grid-search --harmonized-folder ./ --masked-folder ./masked_zscore/ --imputed-folder ./imputed_gnomad/ --output-path ./raiss_report --eigen-ratio-grid '[0.000001, 0.1, 0.001]' --ld-threshold-grid '[0,10]' --n-cpu 8
+
+ """
+}
diff --git a/modules/sanity_checks.nf b/modules/sanity_checks.nf
new file mode 100755
index 0000000000000000000000000000000000000000..925416c13527fe38379239883a87fe00c6b6986c
--- /dev/null
+++ b/modules/sanity_checks.nf
@@ -0,0 +1,22 @@
+
+
+
+params.output_folder = "/pasteur/zeus/projets/p02/GGS_JASS/DATA_BATCH_04_11_2022/"
+params.ancestry = ""
+params.harmonized_files = ""
+
+process Sanity_checks {
+ publishDir "${params.output_folder}", pattern: "sanity_checks/*.txt", mode: 'copy'
+ input:
+ path harmonized_files from params.harmonized_files
+ path imputed_files from params.imputed_files
+
+ script:
+ """
+ trait=`cut --delimiter '.' -f 1 <<< ${trait_file}`
+ echo \$trait
+ ls
+ mkdir -p sanity_checks_${params.EUR}
+ raiss sanity-check --trait \${trait} --harmonized-folder ${params.harmonized_files} --imputed-folder ${params.imputed_files} --output-path ./sanity_checks/sanity_report_${params.ancestry}
+ """
+ }