From 0f434659f79da67d3d440c5fb0cb9ea8a1ec5cbd Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 17 Oct 2024 14:18:22 -0500
Subject: Add `speciesid` and `populationid` arguments to the script.

---
 scripts/rqtl2/phenotypes_qc.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index 9d58137..f602681 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -2,7 +2,6 @@
 import sys
 import tempfile
 from pathlib import Path
-from argparse import ArgumentParser
 from zipfile import ZipFile
 from logging import Logger, getLogger, StreamHandler
 
@@ -12,10 +11,10 @@ from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
 from r_qtl import exceptions as rqe
 
-from scripts.cli_parser import init_cli_parser
 from uploader.files import sha256_digest_over_file
 from scripts.rqtl2.entry import build_main
 from scripts.rqtl2.cli_parser import add_bundle_argument
+from scripts.cli_parser import init_cli_parser, add_global_data_arguments
 
 def validate(phenobundle: Path, logger: Logger) -> dict:
     """Check that the bundle is generally valid"""
@@ -125,10 +124,10 @@ if __name__ == "__main__":
 
     def cli_args():
         """Process command-line arguments for `install_phenos`"""
-        parser = add_bundle_argument(init_cli_parser(
+        parser = add_bundle_argument(add_global_data_arguments(init_cli_parser(
             program="PhenotypesQC",
             description=(
-                "Perform Quality Control checks on a phenotypes bundle file")))
+                "Perform Quality Control checks on a phenotypes bundle file"))))
         parser.add_argument(
             "--working-dir",
             default=f"{tempfile.gettempdir()}/phenotypes_qc",
-- 
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