feat: add kGWASflow.py

kGWASflow.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+
+import argparse
+import os
+
+
+# Parse command line arguments
+parser = argparse.ArgumentParser(description='Run kGWASflow')
+parser.add_argument('-c', '--config-file', default='config/config.yaml', help='Path to the config.yaml file (default: config.yaml)')
+# parser.add_argument('--output', type=str, help='Path to output directory')
+parser.add_argument('-t', '--threads', type=int, default=1, help='Number of threads')
+parser.add_argument('--conda-frontend', type=str, default='conda', help='Conda frontend to use')
+parser.add_argument('-n', '--dryrun', action='store_true', help='Dry run', required=False)
+parser.add_argument('--samples', type=str, help='Path to samples.tsv file', required=False)
+parser.add_argument('--phenotypes', type=str, help='Path to phenos.tsv file', required=False)
+parser.add_argument('-r', '--generate-report', action='store_true', help='create an HTML report', required=False)
+parser.add_argument('-v', '--verbose', action='store_true', help='Increase output verbosity', required=False)
+args = parser.parse_args()
+
+# if config file is not specified, use the default config file
+if args.config_file is None:
+    args.config_file = 'config/config.yaml'
+
+# Define the command to run snakemake
+cmd = f'snakemake --use-conda --conda-frontend {args.conda_frontend} --cores {args.threads} --rerun-triggers mtime --rerun-incomplete --configfile {args.config_file}'
+
+if args.dryrun:
+    cmd += ' --dryrun'
+
+# Add the --report flag if specified
+if args.generate_report:
+    if args.dryrun:
+        cmd += ' --report kGWASflow-report.html'
+    if not args.dryrun:
+        cmd += ' --dryrun --report kGWASflow-report.html'
+
+if args.verbose:
+    cmd += ' --verbose'
+
+if __name__ == "__main__":
+    # Run the command
+    os.system(cmd)