diff --git a/pipeline/rules/dependencies.smk b/pipeline/rules/dependencies.smk
index dfb7fad..7234f09 100644
--- a/pipeline/rules/dependencies.smk
+++ b/pipeline/rules/dependencies.smk
@@ -1,713 +1,712 @@
-########
-# Import required packages
-########
-
-import pandas as pd
-from pathlib import Path
-import multiprocessing
-import hashlib
-import sys
-import tempfile
-import os
-import subprocess
-import re
-import glob
-
-######
-# Check genopred conda env is activated
-######
-
-conda_env_name = os.getenv('CONDA_DEFAULT_ENV')
-if not conda_env_name == 'genopred':
-  print("Error: The genopred conda environment must be active when running the pipeline.\nFor more information: https://opain.github.io/GenoPred/pipeline_readme.html#Step_2:_Create_conda_environment_for_pipeline")
-  sys.exit(1)
-
-######
-# Check config file
-######
-
-def check_config_parameters(config):
-    required_params = [
-        'outdir', 'resdir', 'refdir', 'config_file', 'gwas_list', 'target_list',
-        'score_list', 'pgs_methods', 'ptclump_pts', 'dbslmm_h2f', 'prscs_phi',
-        'prscs_ldref', 'ldpred2_model', 'ldpred2_inference', 'ancestry_prob_thresh',
-        'testing'
-    ]
-    
-    missing_params = []
-    for param in required_params:
-        if config.get(param) is None:
-            missing_params.append(param)
-
-    if missing_params:
-        print("Error: Missing parameters in user-specified and default config files:", missing_params)
-        sys.exit(1)
-
-# Check the sample config
-check_config_parameters(config)
-
-# Set outdir parameter
-outdir=config['outdir']
-
-# Set PRS-CS ld reference path
-if config['prscs_ldref'] == 'ukb':
-    prscs_ldref='ukbb'
-elif config['prscs_ldref'] == '1kg':
-    prscs_ldref='1kg'
-
-# Set resdir parameter
-# If resdir is NA, set resdir to 'resources'
-if config['resdir'] == 'NA':
-  resdir='resources'
-else:
-  resdir=config['resdir']
-
-# Set refdir parameter
-# If refdir is NA, set refdir to '${resdir}/data/ref'
-if config['refdir'] == 'NA':
-  refdir=f"{resdir}/data/ref"
-  ref_input=f"{refdir}/ref.pop.txt"
-else:
-  refdir=config['refdir']
-  ref_input = [os.path.join(refdir, f"ref.chr{i}.{ext}") for i in range(1, 23) for ext in ['pgen', 'pvar', 'psam', 'rds']] + \
-                 [os.path.join(refdir, file_name) for file_name in ['ref.pop.txt', 'ref.keep.list']]
-
-  for full_path in ref_input:
-      if not os.path.exists(full_path):
-          raise FileNotFoundError(f"File not found: {full_path}. Check reference data format.")
-
-########
-# Create required functions
-########
-
-# Create function to check whether path of gwas or score exist
-def check_list_paths(df):
-  for index, row in df.iterrows():
-    file_path = row['path']
-    if pd.isna(file_path):
-        continue
-    if not os.path.exists(file_path):
-        raise FileNotFoundError(f"File not found: {file_path}")
-
-# Create function to return the range of chromosomes requested
-def get_chr_range(testing):
-  if testing != 'NA':
-    val = int(testing[-2:])
-    return range(val, val + 1)
-  else:
-    return range(1, 23)
-
-# Create function to check whether path of gwas or score exist
-def check_target_paths(df, chr):
-  for index, row in df.iterrows():
-    if row['type'] == '23andMe':
-      file_path = row['path']
-    if row['type'] == 'plink1':
-      file_path =  row['path'] + ".chr" + chr + ".bed"
-    if row['type'] == 'plink2':
-      file_path =  row['path'] + ".chr" + chr + ".pgen"
-    if row['type'] == 'bgen':
-      file_path =  row['path'] + ".chr" + chr + ".bgen"
-    if row['type'] == 'vcf':
-      file_path =  row['path'] + ".chr" + chr + ".vcf.gz"
-    if not os.path.exists(file_path):
-        raise FileNotFoundError(f"File not found: {file_path}")
-    else :
-      return []
-
-########
-# Check for repo version updates
-########
-
-# If there has been a change to the major or minor version numbers, we will rerun the entire pipeline
-
-# Define the path for storing the last known version
-os.makedirs(resdir, exist_ok=True)
-last_version_file = f"{resdir}/last_version.txt"
-
-def get_current_version():
-    cmd = "git describe --tags"
-    tag = subprocess.check_output(cmd, shell=True).decode().strip()
-    match = re.match(r"v?(\d+)\.(\d+)", tag)
-    if match:
-        return int(match.group(1)), int(match.group(2))  # Major, Minor
-    else:
-        raise ValueError("Git tag does not contain a valid version format.")
-
-def read_last_version():
-    if os.path.exists(last_version_file):
-        with open(last_version_file, "r") as file:
-            major, minor = file.read().strip().split('.')
-            return int(major), int(minor)
-    return 0, 0  # Default to 0.0 if file does not exist
-
-def write_last_version(major, minor):
-    with open(last_version_file, "w") as file:
-        file.write(f"{major}.{minor}")
-
-# Access overwrite flag from config
-overwrite = config.get("overwrite", "false").lower() == "true"
-
-# Main logic to check version and decide on execution
-current_major, current_minor = get_current_version()
-last_major, last_minor = read_last_version()
-
-# Check if the last version is 0.0, proceed without requiring overwrite
-if last_major == 0 and last_minor == 0:
-    print(f"Initial version setup detected. Updating to v{current_major}.{current_minor}.")
-    write_last_version(current_major, current_minor)
-else:
-    # Check for both major and minor version changes
-    if current_major != last_major or current_minor != last_minor:
-        if not overwrite:
-            print(f"Change in version of GenoPred detected from v{last_major}.{last_minor} to v{current_major}.{current_minor}. Use --config overwrite=true to proceed.")
-            sys.exit(1)
-        else:
-            print("Proceeding with version update due to overwrite=true config.")
-            write_last_version(current_major, current_minor)  # Update the stored version
-
-########
-# Download dependencies
-########
-
-# Download impute2_data
-rule download_impute2_data:
-  output:
-    directory(f"{resdir}/data/impute2/1000GP_Phase3")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_impute2_data.txt"
-  log:
-    f"{resdir}/data/logs/download_impute2_data.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/data/impute2; \
-      mkdir -p {resdir}/data/impute2/; \
-      wget --no-check-certificate -O {resdir}/data/impute2/1000GP_Phase3.tgz https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz; \
-      tar -zxvf {resdir}/data/impute2/1000GP_Phase3.tgz -C {resdir}/data/impute2/; \
-      rm {resdir}/data/impute2/1000GP_Phase3.tgz; \
-      wget --no-check-certificate -O {resdir}/data/impute2/1000GP_Phase3_chrX.tgz https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3_chrX.tgz; \
-      tar -zxvf {resdir}/data/impute2/1000GP_Phase3_chrX.tgz -C {resdir}/data/impute2/1000GP_Phase3/; \
-      rm {resdir}/data/impute2/1000GP_Phase3_chrX.tgz
-    }} > {log} 2>&1
-    """
-
-# Download PLINK. DBSLMM requires the binary to be specified, which is challenging with conda environments. I have tried to avoid this again but no joy. The conda environment may not exist when the snakemake is executed which will cause problems if trying to access the conda environment manually.
-rule download_plink:
-  output:
-    f"{resdir}/software/plink/plink"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_plink.txt"
-  log:
-    f"{resdir}/data/logs/download_plink.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/software/plink; \
-      mkdir -p {resdir}/software/plink; \
-      wget --no-check-certificate -O {resdir}/software/plink/plink_linux_x86_64_20210606.zip https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip; \
-      unzip {resdir}/software/plink/plink_linux_x86_64_20210606.zip -d {resdir}/software/plink; \
-      rm {resdir}/software/plink/plink_linux_x86_64_20210606.zip
-    }} > {log} 2>&1
-    """
-
-# Download LDSC
-rule download_ldsc:
-  output:
-    f"{resdir}/software/ldsc/ldsc.py"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldsc.txt"
-  log:
-    f"{resdir}/data/logs/download_ldsc.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/software/ldsc; \
-      git clone https://github.com/bulik/ldsc.git {resdir}/software/ldsc/; \
-      cd {resdir}/software/ldsc/; \
-      git reset --hard aa33296abac9569a6422ee6ba7eb4b902422cc74
-    }} > {log} 2>&1
-    """
-
-# Download ld scores from PanUKB
-rule download_ldscores_panukb:
-  output:
-    directory(f"{resdir}/data/ld_scores")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldscores_panukb.txt"
-  log:
-    f"{resdir}/data/logs/download_ldscores_panukb.log"
-  shell:
-    """
-    {{
-      mkdir -p {resdir}/data/ld_scores; \
-      wget --no-check-certificate -O {resdir}/data/ld_scores.tar.gz https://zenodo.org/records/10666891/files/ld_scores.tar.gz?download=1; \
-      tar -xvf {resdir}/data/ld_scores.tar.gz -C {resdir}/data/; \
-      rm {resdir}/data/ld_scores.tar.gz
-    }} > {log} 2>&1
-    """
-
-# Download hapmap3 snplist
-rule download_hm3_snplist:
-  output:
-    f"{resdir}/data/hm3_snplist/w_hm3.snplist"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_hm3_snplist.txt"
-  log:
-    f"{resdir}/data/logs/download_hm3_snplist.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/data/hm3_snplist; \
-      mkdir -p {resdir}/data/hm3_snplist; \
-      wget --no-check-certificate -O {resdir}/data/hm3_snplist/w_hm3.snplist.gz https://zenodo.org/record/7773502/files/w_hm3.snplist.gz?download=1; \
-      gunzip {resdir}/data/hm3_snplist/w_hm3.snplist.gz
-    }} > {log} 2>&1
-    """
-
-# Download DBSLMM
-rule download_dbslmm:
-  output:
-    directory(f"{resdir}/software/dbslmm/")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_dbslmm.txt"
-  conda:
-    "../envs/analysis.yaml"
-  log:
-    f"{resdir}/data/logs/download_dbslmm.log"
-  shell:
-    """
-    {{
-      git clone https://github.com/biostat0903/DBSLMM.git {output}; \
-      cd {output}; \
-      git reset --hard d158a144dd2f2dc883ad93d0ea71e8fc48e80bd3; \
-      wget --no-check-certificate -O software/dbslmm "https://drive.usercontent.google.com/download?id=1eAbEyhF8rO_faOFL3jqRo9LmfgJNRH6K&export=download&authuser=0"; \
-      chmod a+x software/dbslmm
-    }} > {log} 2>&1
-    """
-
-# Download LD block data
-rule download_ld_blocks:
-  output:
-    directory(f"{resdir}/data/ld_blocks/")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ld_blocks.txt"
-  log:
-    f"{resdir}/data/logs/download_ld_blocks.log"
-  shell:
-    """
-    {{
-      git clone https://bitbucket.org/nygcresearch/ldetect-data.git {output}; \
-      mv {resdir}/data/ld_blocks/ASN {resdir}/data/ld_blocks/EAS
-    }} > {log} 2>&1
-    """
-
-# Download UKB-based PRScs reference
-# Note. Using Yengo Height GWAS with OpenSNP target, using the UKB reference performed significantly worse than the 1KG reference.
-prscs_ref_ukb_dropbox = {
-    'eur': 'https://www.dropbox.com/s/t9opx2ty6ucrpib/ldblk_ukbb_eur.tar.gz?dl=0',
-    'eas': 'https://www.dropbox.com/s/fz0y3tb9kayw8oq/ldblk_ukbb_eas.tar.gz?dl=0',
-    'afr': 'https://www.dropbox.com/s/dtccsidwlb6pbtv/ldblk_ukbb_afr.tar.gz?dl=0',
-    'amr': 'https://www.dropbox.com/s/y7ruj364buprkl6/ldblk_ukbb_amr.tar.gz?dl=0',
-    'sas': 'https://www.dropbox.com/s/nto6gdajq8qfhh0/ldblk_ukbb_sas.tar.gz?dl=0',
-}
-
-rule download_prscs_ref_ukb:
-  output:
-    f"{resdir}/data/prscs_ref/ldblk_ukbb_{{population}}/ldblk_ukbb_chr1.hdf5"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_prscs_ref_ukb-{{population}}.txt"
-  log:
-    f"{resdir}/data/logs/download_prscs_ref_ukb-{{population}}.log"
-  params:
-    url=lambda w: prscs_ref_ukb_dropbox.get(w.population)
-  shell:
-    """
-    {{
-      mkdir -p {resdir}/data/prscs_ref; \
-      rm -r -f {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}; \
-      wget --no-check-certificate -O {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz {params.url}; \
-      tar -zxvf {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/; \
-      rm {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz
-    }} > {log} 2>&1
-    """
-
-rule download_prscs_ref_ukb_all:
-  input:
-    lambda w: expand(f"{resdir}/data/prscs_ref/ldblk_ukbb_{{population}}/ldblk_ukbb_chr1.hdf5", population=['eur','eas','afr','amr','sas'])
-
-# Download 1KG-based PRScs reference
-prscs_ref_1kg_dropbox = {
-    'eur': 'https://www.dropbox.com/s/mt6var0z96vb6fv/ldblk_1kg_eur.tar.gz?dl=0',
-    'eas': 'https://www.dropbox.com/s/7ek4lwwf2b7f749/ldblk_1kg_eas.tar.gz?dl=0',
-    'afr': 'https://www.dropbox.com/s/mq94h1q9uuhun1h/ldblk_1kg_afr.tar.gz?dl=0',
-    'amr': 'https://www.dropbox.com/s/uv5ydr4uv528lca/ldblk_1kg_amr.tar.gz?dl=0',
-    'sas': 'https://www.dropbox.com/s/hsm0qwgyixswdcv/ldblk_1kg_sas.tar.gz?dl=0',
-}
-
-rule download_prscs_ref_1kg:
-  output:
-    f"{resdir}/data/prscs_ref/ldblk_1kg_{{population}}/ldblk_1kg_chr1.hdf5"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_prscs_ref_1kg-{{population}}.txt"
-  log:
-    f"{resdir}/data/logs/download_prscs_ref_1kg-{{population}}.log"
-  params:
-    url=lambda w: prscs_ref_1kg_dropbox.get(w.population)
-  shell:
-    """
-    {{
-      mkdir -p {resdir}/data/prscs_ref; \
-      rm -r -f {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}; \
-      wget --no-check-certificate -O {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz {params.url}; \
-      tar -zxvf {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/; \
-      rm {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz
-    }} > {log} 2>&1
-    """
-
-rule download_prscs_ref_1kg_all:
-  input:
-    lambda w: expand(f"{resdir}/data/prscs_ref/ldblk_1kg_{{population}}/ldblk_1kg_chr1.hdf5", population=['eur','eas','afr','amr','sas'])
-
-# Download PRScs software
-rule download_prscs_software:
-  output:
-    directory(f"{resdir}/software/prscs/")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_prscs_software.txt"
-  log:
-    f"{resdir}/data/logs/download_prscs_software.log"
-  shell:
-    """
-    {{
-      git clone https://github.com/getian107/PRScs.git {output}; \
-      cd {output}; \
-      git reset --hard 621fdc80daac56c93d9528eb1a1187f7b1fc9afb
-    }} > {log} 2>&1
-    """
-# Download gctb reference
-rule download_gctb_ref:
-  output:
-    directory(f"{resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_gctb_ref.txt"
-  log:
-    f"{resdir}/data/logs/download_gctb_ref.log"
-  shell:
-    """
-    {{
-      mkdir -p {resdir}/data/gctb_ref; \
-      wget --no-check-certificate -O {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip https://zenodo.org/record/3350914/files/ukbEURu_hm3_sparse.zip?download=1; \
-      unzip {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip -d {resdir}/data/gctb_ref; \
-      for chr in $(seq 1 22);do \
-      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k.ldm.sparse.bin {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_chr${{chr}}.ldm.sparse.bin; \
-      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k.ldm.sparse.info {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_chr${{chr}}.ldm.sparse.info; \
-      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k_sparse.log {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_sparse_chr${{chr}}.log; \
-      done; \
-      rm {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip
-    }} > {log} 2>&1
-    """
-# Download GCTB
-rule download_gctb_software:
-  output:
-    f"{resdir}/software/gctb/gctb_2.03beta_Linux/gctb"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_gctb_software.txt"
-  log:
-    f"{resdir}/data/logs/download_gctb_software.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/software/gctb; \
-      mkdir -p {resdir}/software/gctb; \
-      wget --no-check-certificate -O {resdir}/software/gctb/gctb_2.03beta_Linux.zip https://cnsgenomics.com/software/gctb/download/gctb_2.03beta_Linux.zip; \
-      unzip {resdir}/software/gctb/gctb_2.03beta_Linux.zip -d {resdir}/software/gctb; \
-      rm {resdir}/software/gctb/gctb_2.03beta_Linux.zip
-    }} > {log} 2>&1
-    """
-# Download LDpred2 reference
-rule download_ldpred2_ref:
-  output:
-    directory(f"{resdir}/data/ldpred2_ref")
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldpred2_ref.txt"
-  log:
-    f"{resdir}/data/logs/download_ldpred2_ref.log"
-  shell:
-    """
-    {{
-      mkdir -p {resdir}/data/ldpred2_ref; \
-      wget --no-check-certificate -O {resdir}/data/ldpred2_ref/download.zip https://figshare.com/ndownloader/articles/19213299/versions/2; \
-      unzip {resdir}/data/ldpred2_ref/download.zip -d {resdir}/data/ldpred2_ref/; \
-      rm {resdir}/data/ldpred2_ref/download.zip; \
-      unzip {resdir}/data/ldpred2_ref/ldref_with_blocks.zip -d {resdir}/data/ldpred2_ref/; \
-      mv {resdir}/data/ldpred2_ref/ldref/* {resdir}/data/ldpred2_ref/; \
-      rm {resdir}/data/ldpred2_ref/ldref_with_blocks.zip; \
-      rm -r {resdir}/data/ldpred2_ref/ldref
-    }} > {log} 2>&1
-    """
-# Download LDAK
-rule download_ldak:
-  output:
-    f"{resdir}/software/ldak/ldak5.1.linux"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldak.txt"
-  log:
-    f"{resdir}/data/logs/download_ldak.log"
-  shell:
-    """
-    {{
-      rm -r {resdir}/software/ldak; \
-      mkdir -p {resdir}/software/ldak; \
-      wget --no-check-certificate -O {resdir}/software/ldak/ldak5.1.linux_.zip https://dougspeed.com/wp-content/uploads/ldak5.1.linux_.zip; \
-      unzip {resdir}/software/ldak/ldak5.1.linux_.zip -d {resdir}/software/ldak/; \
-      rm {resdir}/software/ldak/ldak5.1.linux_.zip
-    }} > {log} 2>&1
-    """
-# Download LDAK map data
-rule download_ldak_map:
-  output:
-    f"{resdir}/data/ldak_map/genetic_map_b37/genetic_map_chr22_combined_b37.txt"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldak_map.txt"
-  log:
-    f"{resdir}/data/logs/download_ldak_map.log"
-  shell:
-    """
-    {{
-      rm -r {resdir}/data/ldak_map; \
-      mkdir -p {resdir}/data/ldak_map; \
-      wget --no-check-certificate -O {resdir}/data/ldak_map/genetic_map_b37.zip https://www.dropbox.com/s/slchsd0uyd4hii8/genetic_map_b37.zip; \
-      unzip {resdir}/data/ldak_map/genetic_map_b37.zip -d {resdir}/data/ldak_map/; \
-      rm {resdir}/data/ldak_map/genetic_map_b37.zip
-    }} > {log} 2>&1
-    """
-# Download LDAK bld snp annotations
-rule download_ldak_bld:
-  output:
-    f"{resdir}/data/ldak_bld/README.txt"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldak_bld.txt"
-  log:
-    f"{resdir}/data/logs/download_ldak_bld.log"
-  shell:
-    """
-    {{
-      rm -r {resdir}/data/ldak_bld; \
-      mkdir -p {resdir}/data/ldak_bld; \
-      wget --no-check-certificate -O {resdir}/data/ldak_bld/bld.zip https://genetics.ghpc.au.dk/doug/bld.zip; \
-      unzip {resdir}/data/ldak_bld/bld.zip -d {resdir}/data/ldak_bld/; \
-      rm {resdir}/data/ldak_bld/bld.zip
-    }} > {log} 2>&1
-    """
-# Download LDAK high ld regions file
-rule download_ldak_highld:
-  output:
-    f"{resdir}/data/ldak_highld/highld.txt"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_ldak_highld.txt"
-  log:
-    f"{resdir}/data/logs/download_ldak_highld.log"
-  shell:
-    """
-    {{
-      rm -r {resdir}/data/ldak_highld; \
-      mkdir -p {resdir}/data/ldak_highld; \
-      wget --no-check-certificate -O {resdir}/data/ldak_highld/highld.txt https://dougspeed.com/wp-content/uploads/highld.txt
-    }} > {log} 2>&1
-    """
-
-# Download preprocessed reference data (1KG+HGDP HapMap3)
-rule download_default_ref:
-  output:
-    f"{resdir}/data/ref/ref.pop.txt"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_default_ref.txt"
-  log:
-    f"{resdir}/data/logs/download_default_ref.log"
-  shell:
-    """
-    {{
-      rm -r {resdir}/data/ref; \
-      mkdir -p {resdir}/data/ref; \
-      wget --no-check-certificate -O {resdir}/data/ref/genopred_1kg_hgdp.tar.gz https://zenodo.org/records/10666983/files/genopred_1kg_hgdp.tar.gz?download=1; \
-      tar -xzvf {resdir}/data/ref/genopred_1kg_hgdp.tar.gz -C {resdir}/data/ref/; \
-      mv {resdir}/data/ref/ref/* {resdir}/data/ref/; \
-      rm -r {resdir}/data/ref/ref; \
-      rm {resdir}/data/ref/genopred_1kg_hgdp.tar.gz
-    }} > {log} 2>&1
-    """
-
-# install ggchicklet
-rule install_ggchicklet:
-  input:
-    "envs/analysis.yaml"
-  output:
-    touch("resources/software/install_ggchicklet.done")
-  conda:
-    "../envs/analysis.yaml"
-  benchmark:
-    "resources/data/benchmarks/install_ggchicklet.txt"
-  log:
-    "resources/data/logs/install_ggchicklet.log"
-  shell:
-    """
-    {{
-      Rscript -e 'remotes::install_github(\"hrbrmstr/ggchicklet@64c468dd0900153be1690dbfc5cfb35710da8183\")'
-    }} > {log} 2>&1
-    """
-# install lassosum
-rule install_lassosum:
-  input:
-    "envs/analysis.yaml"
-  output:
-    touch("resources/software/install_lassosum.done")
-  conda:
-    "../envs/analysis.yaml"
-  benchmark:
-    "resources/data/benchmarks/install_lassosum.txt"
-  log:
-    "resources/data/logs/install_lassosum.log"
-  shell:
-    """
-    {{
-      Rscript -e 'remotes::install_github(\"tshmak/lassosum@v0.4.5\")'
-    }} > {log} 2>&1
-    """
-# Install GenoUtils
-rule install_genoutils:
-  input:
-    "envs/analysis.yaml"
-  output:
-    touch("resources/software/install_genoutils.done")
-  conda:
-    "../envs/analysis.yaml"
-  benchmark:
-    "resources/data/benchmarks/install_genoutils.txt"
-  log:
-    "resources/data/logs/install_genoutils.log"
-  shell:
-    """
-    {{
-      Rscript -e 'devtools::install_github(\"opain/GenoUtils@4beb75620f3291b633598acd06febb22298418c8\")'
-    }} > {log} 2>&1
-    """
-
-# Install R packages (handy function for when conda env updates erroneously)
-rule install_r_packages:
-  input:
-    rules.install_ggchicklet.output,
-    rules.install_lassosum.output,
-    rules.install_genoutils.output
-
-# Download pgscatalog_utils
-rule download_pgscatalog_utils:
-  output:
-    f"{resdir}/software/pgscatalog_utils/download_pgscatalog_utils.done"
-  conda:
-    "../envs/pgscatalog_utils.yaml"
-  benchmark:
-    f"{resdir}/data/benchmarks/download_pgscatalog_utils.txt"
-  log:
-    f"{resdir}/data/logs/download_pgscatalog_utils.log"
-  shell:
-    """
-    {{
-      rm -r -f {resdir}/software/pgscatalog_utils; \
-      git clone https://github.com/PGScatalog/pgscatalog_utils.git {resdir}/software/pgscatalog_utils; \
-      cd {resdir}/software/pgscatalog_utils; \
-      git reset --hard 6da7eb0e157ba4e73f941233ee8d8ae4fb5e3926; \
-      poetry install; \
-      poetry build; \
-      pip3 install --user dist/*.whl; \
-      download_scorefiles -h > download_pgscatalog_utils.done
-    }} > {log} 2>&1
-    """
-    
-############
-# Check all dependencies are available
-############
-
-# Rule to install and download commonly required software and data dependencies
-rule get_dependencies:
-  input:
-    rules.download_plink.output,
-    rules.download_ldscores_panukb.output,
-    rules.download_ldsc.output,
-    rules.download_hm3_snplist.output,
-    rules.download_default_ref.output,
-    rules.download_dbslmm.output,
-    rules.download_ld_blocks.output,
-    rules.install_ggchicklet.output,
-    rules.install_lassosum.output,
-    rules.install_genoutils.output,
-    rules.download_pgscatalog_utils.output
-  output:
-    touch(f"{resdir}/software/get_dependencies.done")
-
-############
-# Rules for preparing offline resources
-############
-
-rule get_all_resources:
-  input:
-    rules.download_plink.output,
-    rules.download_ldsc.output,
-    rules.download_dbslmm.output,
-    rules.download_prscs_software.output,
-    rules.download_gctb_software.output,
-    rules.download_ldak.output,
-    rules.download_ldscores_panukb.output,
-    rules.download_hm3_snplist.output,
-    rules.download_ld_blocks.output,
-    rules.download_prscs_ref_ukb_all.input,
-    rules.download_prscs_ref_1kg_all.input,
-    rules.download_gctb_ref.output,
-    rules.download_ldpred2_ref.output,
-    rules.download_ldak_map.output,
-    rules.download_ldak_bld.output,
-    rules.download_ldak_highld.output,
-    rules.download_default_ref.output
-  output:
-    touch(f"{resdir}/software/get_all_resources.done")
-
-rule get_key_resources:
-  input:
-    rules.download_plink.output,
-    rules.download_ldsc.output,
-    rules.download_dbslmm.output,
-    rules.download_ldak.output,
-    rules.download_ldscores_panukb.output,
-    rules.download_hm3_snplist.output,
-    rules.download_ld_blocks.output,
-    rules.download_ldak_map.output,
-    rules.download_ldak_bld.output,
-    rules.download_ldak_highld.output,
-    rules.download_default_ref.output
-  output:
-    touch(f"{resdir}/software/get_key_resources.done")
-
-rule get_prscs_resources:
-  input:
-    rules.get_key_resources.output,
-    rules.download_prscs_software.output,
-    rules.download_prscs_ref_ukb_all.input,
-    rules.download_prscs_ref_1kg_all.input
-  output:
-    touch(f"{resdir}/software/get_prscs_resources.done")
-
-rule get_ldpred2_resources:
-  input:
-    rules.get_key_resources.output,
-    rules.download_ldpred2_ref.output
-  output:
-    touch(f"{resdir}/software/get_ldpred2_resources.done")
-
-rule get_sbayesr_resources:
-  input:
-    rules.get_key_resources.output,
-    rules.download_gctb_software.output,
-    rules.download_gctb_ref.output
-  output:
-    touch(f"{resdir}/software/get_sbayesr_resources.done")
-    
\ No newline at end of file
+########
+# Import required packages
+########
+
+import pandas as pd
+from pathlib import Path
+import multiprocessing
+import hashlib
+import sys
+import tempfile
+import os
+import subprocess
+import re
+import glob
+
+######
+# Check genopred conda env is activated
+######
+
+conda_env_name = os.getenv('CONDA_DEFAULT_ENV')
+if not conda_env_name == 'genopred':
+  print("Error: The genopred conda environment must be active when running the pipeline.\nFor more information: https://opain.github.io/GenoPred/pipeline_readme.html#Step_2:_Create_conda_environment_for_pipeline")
+  sys.exit(1)
+
+######
+# Check config file
+######
+
+def check_config_parameters(config):
+    required_params = [
+        'outdir', 'resdir', 'refdir', 'config_file', 'gwas_list', 'target_list',
+        'score_list', 'pgs_methods', 'ptclump_pts', 'dbslmm_h2f', 'prscs_phi',
+        'prscs_ldref', 'ldpred2_model', 'ldpred2_inference', 'ancestry_prob_thresh',
+        'testing'
+    ]
+
+    missing_params = []
+    for param in required_params:
+        if config.get(param) is None:
+            missing_params.append(param)
+
+    if missing_params:
+        print("Error: Missing parameters in user-specified and default config files:", missing_params)
+        sys.exit(1)
+
+# Check the sample config
+check_config_parameters(config)
+
+# Set outdir parameter
+outdir=config['outdir']
+
+# Set PRS-CS ld reference path
+if config['prscs_ldref'] == 'ukb':
+    prscs_ldref='ukbb'
+elif config['prscs_ldref'] == '1kg':
+    prscs_ldref='1kg'
+
+# Set resdir parameter
+# If resdir is NA, set resdir to 'resources'
+if config['resdir'] == 'NA':
+  resdir='resources'
+else:
+  resdir=config['resdir']
+
+# Set refdir parameter
+# If refdir is NA, set refdir to '${resdir}/data/ref'
+if config['refdir'] == 'NA':
+  refdir=f"{resdir}/data/ref"
+  ref_input=f"{refdir}/ref.pop.txt"
+else:
+  refdir=config['refdir']
+  ref_input = [os.path.join(refdir, f"ref.chr{i}.{ext}") for i in range(1, 23) for ext in ['pgen', 'pvar', 'psam', 'rds']] + \
+                 [os.path.join(refdir, file_name) for file_name in ['ref.pop.txt', 'ref.keep.list']]
+
+  for full_path in ref_input:
+      if not os.path.exists(full_path):
+          raise FileNotFoundError(f"File not found: {full_path}. Check reference data format.")
+
+########
+# Create required functions
+########
+
+# Create function to check whether path of gwas or score exist
+def check_list_paths(df):
+  for index, row in df.iterrows():
+    file_path = row['path']
+    if pd.isna(file_path):
+        continue
+    if not os.path.exists(file_path):
+        raise FileNotFoundError(f"File not found: {file_path}")
+
+# Create function to return the range of chromosomes requested
+def get_chr_range(testing):
+  if testing != 'NA':
+    val = int(testing[-2:])
+    return range(val, val + 1)
+  else:
+    return range(1, 23)
+
+# Create function to check whether path of gwas or score exist
+def check_target_paths(df, chr):
+  for index, row in df.iterrows():
+    if row['type'] == '23andMe':
+      file_path = row['path']
+    if row['type'] == 'plink1':
+      file_path =  row['path'] + ".chr" + chr + ".bed"
+    if row['type'] == 'plink2':
+      file_path =  row['path'] + ".chr" + chr + ".pgen"
+    if row['type'] == 'bgen':
+      file_path =  row['path'] + ".chr" + chr + ".bgen"
+    if row['type'] == 'vcf':
+      file_path =  row['path'] + ".chr" + chr + ".vcf.gz"
+    if not os.path.exists(file_path):
+        raise FileNotFoundError(f"File not found: {file_path}")
+    else :
+      return []
+
+########
+# Check for repo version updates
+########
+
+# If there has been a change to the major or minor version numbers, we will rerun the entire pipeline
+
+# Define the path for storing the last known version
+os.makedirs(resdir, exist_ok=True)
+last_version_file = f"{resdir}/last_version.txt"
+
+def get_current_version():
+    cmd = "git describe --tags"
+    tag = subprocess.check_output(cmd, shell=True).decode().strip()
+    match = re.match(r"v?(\d+)\.(\d+)", tag)
+    if match:
+        return int(match.group(1)), int(match.group(2))  # Major, Minor
+    else:
+        raise ValueError("Git tag does not contain a valid version format.")
+
+def read_last_version():
+    if os.path.exists(last_version_file):
+        with open(last_version_file, "r") as file:
+            major, minor = file.read().strip().split('.')
+            return int(major), int(minor)
+    return 0, 0  # Default to 0.0 if file does not exist
+
+def write_last_version(major, minor):
+    with open(last_version_file, "w") as file:
+        file.write(f"{major}.{minor}")
+
+# Access overwrite flag from config
+overwrite = config.get("overwrite", "false").lower() == "true"
+
+# Main logic to check version and decide on execution
+current_major, current_minor = get_current_version()
+last_major, last_minor = read_last_version()
+
+# Check if the last version is 0.0, proceed without requiring overwrite
+if last_major == 0 and last_minor == 0:
+    print(f"Initial version setup detected. Updating to v{current_major}.{current_minor}.")
+    write_last_version(current_major, current_minor)
+else:
+    # Check for both major and minor version changes
+    if current_major != last_major or current_minor != last_minor:
+        if not overwrite:
+            print(f"Change in version of GenoPred detected from v{last_major}.{last_minor} to v{current_major}.{current_minor}. Use --config overwrite=true to proceed.")
+            sys.exit(1)
+        else:
+            print("Proceeding with version update due to overwrite=true config.")
+            write_last_version(current_major, current_minor)  # Update the stored version
+
+########
+# Download dependencies
+########
+
+# Download impute2_data
+rule download_impute2_data:
+  output:
+    directory(f"{resdir}/data/impute2/1000GP_Phase3")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_impute2_data.txt"
+  log:
+    f"{resdir}/data/logs/download_impute2_data.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/data/impute2; \
+      mkdir -p {resdir}/data/impute2/; \
+      wget --no-check-certificate -O {resdir}/data/impute2/1000GP_Phase3.tgz https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz; \
+      tar -zxvf {resdir}/data/impute2/1000GP_Phase3.tgz -C {resdir}/data/impute2/; \
+      rm {resdir}/data/impute2/1000GP_Phase3.tgz; \
+      wget --no-check-certificate -O {resdir}/data/impute2/1000GP_Phase3_chrX.tgz https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3_chrX.tgz; \
+      tar -zxvf {resdir}/data/impute2/1000GP_Phase3_chrX.tgz -C {resdir}/data/impute2/1000GP_Phase3/; \
+      rm {resdir}/data/impute2/1000GP_Phase3_chrX.tgz
+    }} > {log} 2>&1
+    """
+
+# Download PLINK. DBSLMM requires the binary to be specified, which is challenging with conda environments. I have tried to avoid this again but no joy. The conda environment may not exist when the snakemake is executed which will cause problems if trying to access the conda environment manually.
+rule download_plink:
+  output:
+    f"{resdir}/software/plink/plink"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_plink.txt"
+  log:
+    f"{resdir}/data/logs/download_plink.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/software/plink; \
+      mkdir -p {resdir}/software/plink; \
+      wget --no-check-certificate -O {resdir}/software/plink/plink_linux_x86_64_20210606.zip https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip; \
+      unzip {resdir}/software/plink/plink_linux_x86_64_20210606.zip -d {resdir}/software/plink; \
+      rm {resdir}/software/plink/plink_linux_x86_64_20210606.zip
+    }} > {log} 2>&1
+    """
+
+# Download LDSC
+rule download_ldsc:
+  output:
+    f"{resdir}/software/ldsc/ldsc.py"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldsc.txt"
+  log:
+    f"{resdir}/data/logs/download_ldsc.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/software/ldsc; \
+      git clone https://github.com/bulik/ldsc.git {resdir}/software/ldsc/; \
+      cd {resdir}/software/ldsc/; \
+      git reset --hard aa33296abac9569a6422ee6ba7eb4b902422cc74
+    }} > {log} 2>&1
+    """
+
+# Download ld scores from PanUKB
+rule download_ldscores_panukb:
+  output:
+    directory(f"{resdir}/data/ld_scores")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldscores_panukb.txt"
+  log:
+    f"{resdir}/data/logs/download_ldscores_panukb.log"
+  shell:
+    """
+    {{
+      mkdir -p {resdir}/data/ld_scores; \
+      wget --no-check-certificate -O {resdir}/data/ld_scores.tar.gz https://zenodo.org/records/10666891/files/ld_scores.tar.gz?download=1; \
+      tar -xvf {resdir}/data/ld_scores.tar.gz -C {resdir}/data/; \
+      rm {resdir}/data/ld_scores.tar.gz
+    }} > {log} 2>&1
+    """
+
+# Download hapmap3 snplist
+rule download_hm3_snplist:
+  output:
+    f"{resdir}/data/hm3_snplist/w_hm3.snplist"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_hm3_snplist.txt"
+  log:
+    f"{resdir}/data/logs/download_hm3_snplist.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/data/hm3_snplist; \
+      mkdir -p {resdir}/data/hm3_snplist; \
+      wget --no-check-certificate -O {resdir}/data/hm3_snplist/w_hm3.snplist.gz https://zenodo.org/record/7773502/files/w_hm3.snplist.gz?download=1; \
+      gunzip {resdir}/data/hm3_snplist/w_hm3.snplist.gz
+    }} > {log} 2>&1
+    """
+
+# Download DBSLMM
+rule download_dbslmm:
+  output:
+    directory(f"{resdir}/software/dbslmm/")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_dbslmm.txt"
+  conda:
+    "../envs/analysis.yaml"
+  log:
+    f"{resdir}/data/logs/download_dbslmm.log"
+  shell:
+    """
+    {{
+      git clone https://github.com/biostat0903/DBSLMM.git {output}; \
+      cd {output}; \
+      git reset --hard d158a144dd2f2dc883ad93d0ea71e8fc48e80bd3; \
+      wget --no-check-certificate -O software/dbslmm "https://drive.usercontent.google.com/download?id=1eAbEyhF8rO_faOFL3jqRo9LmfgJNRH6K&export=download&authuser=0"; \
+      chmod a+x software/dbslmm
+    }} > {log} 2>&1
+    """
+
+# Download LD block data
+rule download_ld_blocks:
+  output:
+    directory(f"{resdir}/data/ld_blocks/")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ld_blocks.txt"
+  log:
+    f"{resdir}/data/logs/download_ld_blocks.log"
+  shell:
+    """
+    {{
+      git clone https://bitbucket.org/nygcresearch/ldetect-data.git {output}; \
+      mv {resdir}/data/ld_blocks/ASN {resdir}/data/ld_blocks/EAS
+    }} > {log} 2>&1
+    """
+
+# Download UKB-based PRScs reference
+# Note. Using Yengo Height GWAS with OpenSNP target, using the UKB reference performed significantly worse than the 1KG reference.
+prscs_ref_ukb_dropbox = {
+    'eur': 'https://www.dropbox.com/s/t9opx2ty6ucrpib/ldblk_ukbb_eur.tar.gz?dl=0',
+    'eas': 'https://www.dropbox.com/s/fz0y3tb9kayw8oq/ldblk_ukbb_eas.tar.gz?dl=0',
+    'afr': 'https://www.dropbox.com/s/dtccsidwlb6pbtv/ldblk_ukbb_afr.tar.gz?dl=0',
+    'amr': 'https://www.dropbox.com/s/y7ruj364buprkl6/ldblk_ukbb_amr.tar.gz?dl=0',
+    'sas': 'https://www.dropbox.com/s/nto6gdajq8qfhh0/ldblk_ukbb_sas.tar.gz?dl=0',
+}
+
+rule download_prscs_ref_ukb:
+  output:
+    f"{resdir}/data/prscs_ref/ldblk_ukbb_{{population}}/ldblk_ukbb_chr1.hdf5"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_prscs_ref_ukb-{{population}}.txt"
+  log:
+    f"{resdir}/data/logs/download_prscs_ref_ukb-{{population}}.log"
+  params:
+    url=lambda w: prscs_ref_ukb_dropbox.get(w.population)
+  shell:
+    """
+    {{
+      mkdir -p {resdir}/data/prscs_ref; \
+      rm -r -f {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}; \
+      wget --no-check-certificate -O {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz {params.url}; \
+      tar -zxvf {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/; \
+      rm {resdir}/data/prscs_ref/ldblk_ukbb_{wildcards.population}.tar.gz
+    }} > {log} 2>&1
+    """
+
+rule download_prscs_ref_ukb_all:
+  input:
+    lambda w: expand(f"{resdir}/data/prscs_ref/ldblk_ukbb_{{population}}/ldblk_ukbb_chr1.hdf5", population=['eur','eas','afr','amr','sas'])
+
+# Download 1KG-based PRScs reference
+prscs_ref_1kg_dropbox = {
+    'eur': 'https://www.dropbox.com/s/mt6var0z96vb6fv/ldblk_1kg_eur.tar.gz?dl=0',
+    'eas': 'https://www.dropbox.com/s/7ek4lwwf2b7f749/ldblk_1kg_eas.tar.gz?dl=0',
+    'afr': 'https://www.dropbox.com/s/mq94h1q9uuhun1h/ldblk_1kg_afr.tar.gz?dl=0',
+    'amr': 'https://www.dropbox.com/s/uv5ydr4uv528lca/ldblk_1kg_amr.tar.gz?dl=0',
+    'sas': 'https://www.dropbox.com/s/hsm0qwgyixswdcv/ldblk_1kg_sas.tar.gz?dl=0',
+}
+
+rule download_prscs_ref_1kg:
+  output:
+    f"{resdir}/data/prscs_ref/ldblk_1kg_{{population}}/ldblk_1kg_chr1.hdf5"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_prscs_ref_1kg-{{population}}.txt"
+  log:
+    f"{resdir}/data/logs/download_prscs_ref_1kg-{{population}}.log"
+  params:
+    url=lambda w: prscs_ref_1kg_dropbox.get(w.population)
+  shell:
+    """
+    {{
+      mkdir -p {resdir}/data/prscs_ref; \
+      rm -r -f {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}; \
+      wget --no-check-certificate -O {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz {params.url}; \
+      tar -zxvf {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz -C {resdir}/data/prscs_ref/; \
+      rm {resdir}/data/prscs_ref/ldblk_1kg_{wildcards.population}.tar.gz
+    }} > {log} 2>&1
+    """
+
+rule download_prscs_ref_1kg_all:
+  input:
+    lambda w: expand(f"{resdir}/data/prscs_ref/ldblk_1kg_{{population}}/ldblk_1kg_chr1.hdf5", population=['eur','eas','afr','amr','sas'])
+
+# Download PRScs software
+rule download_prscs_software:
+  output:
+    directory(f"{resdir}/software/prscs/")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_prscs_software.txt"
+  log:
+    f"{resdir}/data/logs/download_prscs_software.log"
+  shell:
+    """
+    {{
+      git clone https://github.com/getian107/PRScs.git {output}; \
+      cd {output}; \
+      git reset --hard 621fdc80daac56c93d9528eb1a1187f7b1fc9afb
+    }} > {log} 2>&1
+    """
+# Download gctb reference
+rule download_gctb_ref:
+  output:
+    directory(f"{resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_gctb_ref.txt"
+  log:
+    f"{resdir}/data/logs/download_gctb_ref.log"
+  shell:
+    """
+    {{
+      mkdir -p {resdir}/data/gctb_ref; \
+      wget --no-check-certificate -O {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip https://zenodo.org/record/3350914/files/ukbEURu_hm3_sparse.zip?download=1; \
+      unzip {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip -d {resdir}/data/gctb_ref; \
+      for chr in $(seq 1 22);do \
+      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k.ldm.sparse.bin {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_chr${{chr}}.ldm.sparse.bin; \
+      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k.ldm.sparse.info {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_chr${{chr}}.ldm.sparse.info; \
+      mv {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr${{chr}}_v3_50k_sparse.log {resdir}/data/gctb_ref/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_v3_50k_sparse_chr${{chr}}.log; \
+      done; \
+      rm {resdir}/data/gctb_ref/ukbEURu_hm3_sparse.zip
+    }} > {log} 2>&1
+    """
+# Download GCTB
+rule download_gctb_software:
+  output:
+    f"{resdir}/software/gctb/gctb_2.03beta_Linux/gctb"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_gctb_software.txt"
+  log:
+    f"{resdir}/data/logs/download_gctb_software.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/software/gctb; \
+      mkdir -p {resdir}/software/gctb; \
+      wget --no-check-certificate -O {resdir}/software/gctb/gctb_2.03beta_Linux.zip https://cnsgenomics.com/software/gctb/download/gctb_2.03beta_Linux.zip; \
+      unzip {resdir}/software/gctb/gctb_2.03beta_Linux.zip -d {resdir}/software/gctb; \
+      rm {resdir}/software/gctb/gctb_2.03beta_Linux.zip
+    }} > {log} 2>&1
+    """
+# Download LDpred2 reference
+rule download_ldpred2_ref:
+  output:
+    directory(f"{resdir}/data/ldpred2_ref")
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldpred2_ref.txt"
+  log:
+    f"{resdir}/data/logs/download_ldpred2_ref.log"
+  shell:
+    """
+    {{
+      mkdir -p {resdir}/data/ldpred2_ref; \
+      wget --no-check-certificate -O {resdir}/data/ldpred2_ref/download.zip https://figshare.com/ndownloader/articles/19213299/versions/2; \
+      unzip {resdir}/data/ldpred2_ref/download.zip -d {resdir}/data/ldpred2_ref/; \
+      rm {resdir}/data/ldpred2_ref/download.zip; \
+      unzip {resdir}/data/ldpred2_ref/ldref_with_blocks.zip -d {resdir}/data/ldpred2_ref/; \
+      mv {resdir}/data/ldpred2_ref/ldref/* {resdir}/data/ldpred2_ref/; \
+      rm {resdir}/data/ldpred2_ref/ldref_with_blocks.zip; \
+      rm -r {resdir}/data/ldpred2_ref/ldref
+    }} > {log} 2>&1
+    """
+# Download LDAK
+rule download_ldak:
+  output:
+    f"{resdir}/software/ldak/ldak5.1.linux"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldak.txt"
+  log:
+    f"{resdir}/data/logs/download_ldak.log"
+  shell:
+    """
+    {{
+      rm -r {resdir}/software/ldak; \
+      mkdir -p {resdir}/software/ldak; \
+      wget --no-check-certificate -O {resdir}/software/ldak/ldak5.1.linux_.zip https://dougspeed.com/wp-content/uploads/ldak5.1.linux_.zip; \
+      unzip {resdir}/software/ldak/ldak5.1.linux_.zip -d {resdir}/software/ldak/; \
+      rm {resdir}/software/ldak/ldak5.1.linux_.zip
+    }} > {log} 2>&1
+    """
+# Download LDAK map data
+rule download_ldak_map:
+  output:
+    f"{resdir}/data/ldak_map/genetic_map_b37/genetic_map_chr22_combined_b37.txt"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldak_map.txt"
+  log:
+    f"{resdir}/data/logs/download_ldak_map.log"
+  shell:
+    """
+    {{
+      rm -r {resdir}/data/ldak_map; \
+      mkdir -p {resdir}/data/ldak_map; \
+      wget --no-check-certificate -O {resdir}/data/ldak_map/genetic_map_b37.zip https://www.dropbox.com/s/slchsd0uyd4hii8/genetic_map_b37.zip; \
+      unzip {resdir}/data/ldak_map/genetic_map_b37.zip -d {resdir}/data/ldak_map/; \
+      rm {resdir}/data/ldak_map/genetic_map_b37.zip
+    }} > {log} 2>&1
+    """
+# Download LDAK bld snp annotations
+rule download_ldak_bld:
+  output:
+    f"{resdir}/data/ldak_bld/README.txt"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldak_bld.txt"
+  log:
+    f"{resdir}/data/logs/download_ldak_bld.log"
+  shell:
+    """
+    {{
+      rm -r {resdir}/data/ldak_bld; \
+      mkdir -p {resdir}/data/ldak_bld; \
+      wget --no-check-certificate -O {resdir}/data/ldak_bld/bld.zip https://genetics.ghpc.au.dk/doug/bld.zip; \
+      unzip {resdir}/data/ldak_bld/bld.zip -d {resdir}/data/ldak_bld/; \
+      rm {resdir}/data/ldak_bld/bld.zip
+    }} > {log} 2>&1
+    """
+# Download LDAK high ld regions file
+rule download_ldak_highld:
+  output:
+    f"{resdir}/data/ldak_highld/highld.txt"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_ldak_highld.txt"
+  log:
+    f"{resdir}/data/logs/download_ldak_highld.log"
+  shell:
+    """
+    {{
+      rm -r {resdir}/data/ldak_highld; \
+      mkdir -p {resdir}/data/ldak_highld; \
+      wget --no-check-certificate -O {resdir}/data/ldak_highld/highld.txt https://dougspeed.com/wp-content/uploads/highld.txt
+    }} > {log} 2>&1
+    """
+
+# Download preprocessed reference data (1KG+HGDP HapMap3)
+rule download_default_ref:
+  output:
+    f"{resdir}/data/ref/ref.pop.txt"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_default_ref.txt"
+  log:
+    f"{resdir}/data/logs/download_default_ref.log"
+  shell:
+    """
+    {{
+      rm -r {resdir}/data/ref; \
+      mkdir -p {resdir}/data/ref; \
+      wget --no-check-certificate -O {resdir}/data/ref/genopred_1kg_hgdp.tar.gz https://zenodo.org/records/10666983/files/genopred_1kg_hgdp.tar.gz?download=1; \
+      tar -xzvf {resdir}/data/ref/genopred_1kg_hgdp.tar.gz -C {resdir}/data/ref/; \
+      mv {resdir}/data/ref/ref/* {resdir}/data/ref/; \
+      rm -r {resdir}/data/ref/ref; \
+      rm {resdir}/data/ref/genopred_1kg_hgdp.tar.gz
+    }} > {log} 2>&1
+    """
+
+# install ggchicklet
+rule install_ggchicklet:
+  input:
+    "envs/analysis.yaml"
+  output:
+    touch("resources/software/install_ggchicklet.done")
+  conda:
+    "../envs/analysis.yaml"
+  benchmark:
+    "resources/data/benchmarks/install_ggchicklet.txt"
+  log:
+    "resources/data/logs/install_ggchicklet.log"
+  shell:
+    """
+    {{
+      Rscript -e 'remotes::install_github(\"hrbrmstr/ggchicklet@64c468dd0900153be1690dbfc5cfb35710da8183\")'
+    }} > {log} 2>&1
+    """
+# install lassosum
+rule install_lassosum:
+  input:
+    "envs/analysis.yaml"
+  output:
+    touch("resources/software/install_lassosum.done")
+  conda:
+    "../envs/analysis.yaml"
+  benchmark:
+    "resources/data/benchmarks/install_lassosum.txt"
+  log:
+    "resources/data/logs/install_lassosum.log"
+  shell:
+    """
+    {{
+      Rscript -e 'remotes::install_github(\"tshmak/lassosum@v0.4.5\")'
+    }} > {log} 2>&1
+    """
+# Install GenoUtils
+rule install_genoutils:
+  input:
+    "envs/analysis.yaml"
+  output:
+    touch("resources/software/install_genoutils.done")
+  conda:
+    "../envs/analysis.yaml"
+  benchmark:
+    "resources/data/benchmarks/install_genoutils.txt"
+  log:
+    "resources/data/logs/install_genoutils.log"
+  shell:
+    """
+    {{
+      Rscript -e 'devtools::install_github(\"opain/GenoUtils@50ac8a2078226c8c2349064f904031576fbfe606\")'
+    }} > {log} 2>&1
+    """
+
+# Install R packages (handy function for when conda env updates erroneously)
+rule install_r_packages:
+  input:
+    rules.install_ggchicklet.output,
+    rules.install_lassosum.output,
+    rules.install_genoutils.output
+
+# Download pgscatalog_utils
+rule download_pgscatalog_utils:
+  output:
+    f"{resdir}/software/pgscatalog_utils/download_pgscatalog_utils.done"
+  conda:
+    "../envs/pgscatalog_utils.yaml"
+  benchmark:
+    f"{resdir}/data/benchmarks/download_pgscatalog_utils.txt"
+  log:
+    f"{resdir}/data/logs/download_pgscatalog_utils.log"
+  shell:
+    """
+    {{
+      rm -r -f {resdir}/software/pgscatalog_utils; \
+      git clone https://github.com/PGScatalog/pgscatalog_utils.git {resdir}/software/pgscatalog_utils; \
+      cd {resdir}/software/pgscatalog_utils; \
+      git reset --hard 6da7eb0e157ba4e73f941233ee8d8ae4fb5e3926; \
+      poetry install; \
+      poetry build; \
+      pip3 install --user dist/*.whl; \
+      download_scorefiles -h > download_pgscatalog_utils.done
+    }} > {log} 2>&1
+    """
+
+############
+# Check all dependencies are available
+############
+
+# Rule to install and download commonly required software and data dependencies
+rule get_dependencies:
+  input:
+    rules.download_plink.output,
+    rules.download_ldscores_panukb.output,
+    rules.download_ldsc.output,
+    rules.download_hm3_snplist.output,
+    rules.download_default_ref.output,
+    rules.download_dbslmm.output,
+    rules.download_ld_blocks.output,
+    rules.install_ggchicklet.output,
+    rules.install_lassosum.output,
+    rules.install_genoutils.output,
+    rules.download_pgscatalog_utils.output
+  output:
+    touch(f"{resdir}/software/get_dependencies.done")
+
+############
+# Rules for preparing offline resources
+############
+
+rule get_all_resources:
+  input:
+    rules.download_plink.output,
+    rules.download_ldsc.output,
+    rules.download_dbslmm.output,
+    rules.download_prscs_software.output,
+    rules.download_gctb_software.output,
+    rules.download_ldak.output,
+    rules.download_ldscores_panukb.output,
+    rules.download_hm3_snplist.output,
+    rules.download_ld_blocks.output,
+    rules.download_prscs_ref_ukb_all.input,
+    rules.download_prscs_ref_1kg_all.input,
+    rules.download_gctb_ref.output,
+    rules.download_ldpred2_ref.output,
+    rules.download_ldak_map.output,
+    rules.download_ldak_bld.output,
+    rules.download_ldak_highld.output,
+    rules.download_default_ref.output
+  output:
+    touch(f"{resdir}/software/get_all_resources.done")
+
+rule get_key_resources:
+  input:
+    rules.download_plink.output,
+    rules.download_ldsc.output,
+    rules.download_dbslmm.output,
+    rules.download_ldak.output,
+    rules.download_ldscores_panukb.output,
+    rules.download_hm3_snplist.output,
+    rules.download_ld_blocks.output,
+    rules.download_ldak_map.output,
+    rules.download_ldak_bld.output,
+    rules.download_ldak_highld.output,
+    rules.download_default_ref.output
+  output:
+    touch(f"{resdir}/software/get_key_resources.done")
+
+rule get_prscs_resources:
+  input:
+    rules.get_key_resources.output,
+    rules.download_prscs_software.output,
+    rules.download_prscs_ref_ukb_all.input,
+    rules.download_prscs_ref_1kg_all.input
+  output:
+    touch(f"{resdir}/software/get_prscs_resources.done")
+
+rule get_ldpred2_resources:
+  input:
+    rules.get_key_resources.output,
+    rules.download_ldpred2_ref.output
+  output:
+    touch(f"{resdir}/software/get_ldpred2_resources.done")
+
+rule get_sbayesr_resources:
+  input:
+    rules.get_key_resources.output,
+    rules.download_gctb_software.output,
+    rules.download_gctb_ref.output
+  output:
+    touch(f"{resdir}/software/get_sbayesr_resources.done")