scripts: Process R/qtl2 bundle

Build script to start the processing of the R/qtl2 bundle.

1 files changed, 13 insertions, 9 deletions

diff --git a/scripts/cli_parser.py b/scripts/cli_parser.py
index bceb3f4..e8f030c 100644
--- a/scripts/cli_parser.py
+++ b/scripts/cli_parser.py
@@ -7,16 +7,20 @@ def init_cli_parser(program: str, description: Optional[str] = None) -> Argument
     """Initialise the CLI arguments parser."""
     parser = ArgumentParser(prog=program, description=description)
 
-    parser.add_argument("databaseuri", help="URL to MariaDB")
-    parser.add_argument("redisuri", help="URL to Redis")
-    parser.add_argument("jobid",
-                        help="Job ID that this belongs to.",
-                        type=UUID)
-    parser.add_argument("--redisexpiry",
-                        help="How long to keep any redis keys around.",
-                        type=int,
-                        default=86400)
+    parser.add_argument(
+        "databaseuri", type=str, help="URI to connect to MariaDB")
+    parser.add_argument(
+        "redisuri", type=str, help="URI to connect to the redis server.")
+    parser.add_argument("jobid", type=UUID, help="Job ID that this belongs to")
+    parser.add_argument(
+        "--redisexpiry",
+        type=int,
+        default=86400,
+        help="How long to keep any redis keys around.")
+    return parser
 
+def add_global_data_arguments(parser: ArgumentParser) -> ArgumentParser:
+    """Add the global (present in nearly ALL scripts) CLI arguments."""
     parser.add_argument("speciesid",
                         type=int,
                         help="Species to which bundle relates.")