Move repository parameter to main parser. Improve debug output

psot/main.py

@@ -7,15 +7,16 @@ import shutil
 from psot.nextflow import setup_execution_directory, execute_analysis
 import tempfile
 import sys
+import json
 
 def main():
     parser = argparse.ArgumentParser(description='Make bioinformatic observations on aminoacid sequences')
     parser.set_defaults(func=help)
+    parser.add_argument('--repository', '-r', action='append', help='Include the given repository')
 
     subparsers = parser.add_subparsers()
     info_parser = subparsers.add_parser('info')
     info_parser.add_argument('--listanalyses', '-l', action='store_true', help='Show available analysis steps')
-    info_parser.add_argument('--repository', '-r', action='append', help='Include the given repository')
     info_parser.set_defaults(func=info)
 
     analyze_parser = subparsers.add_parser('analyze')
@@ -29,7 +30,6 @@ def main():
     analyze_parser.add_argument('--debug', '-d', action='store_true', help='Debug mode, computation directory will not be removed after computation')
     analyze_parser.add_argument('--execution_dir', '-e', help='Use the specified execution directory and do not delete it after the computation')
     analyze_parser.add_argument('--use_cluster', '-C', action='store_true', help='Use compute cluster for execution')
-    analyze_parser.add_argument('--repository', '-r', action='append', help='Include the given repository')
     analyze_parser.set_defaults(func=analyze)
 
     args = parser.parse_args()
@@ -49,7 +49,7 @@ def analyze(args, config):
       sys.exit(1)
     execution = generate_execution(config, args)
     if args.debug:
-        print(execution)
+        print(json.dumps(execution, indent=2))
     setup_execution_directory(execution)
     execute_analysis(execution)
     cleanup(execution)