From db196d5ea2dd2ffbb6d9ff4b9fcc5dd2b2d66678 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 17 Oct 2024 14:15:03 -0500
Subject: Add the working directory argument to the script.

Add a `--working-dir` argument to allow passing a directory where the
script process the files within. If not provided, it defaults to a
directory within the systems temporary directory.
---
 scripts/rqtl2/phenotypes_qc.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index be57513..9d58137 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -1,5 +1,6 @@
 """Run quality control on phenotypes-specific files in the bundle."""
 import sys
+import tempfile
 from pathlib import Path
 from argparse import ArgumentParser
 from zipfile import ZipFile
@@ -128,6 +129,12 @@ if __name__ == "__main__":
             program="PhenotypesQC",
             description=(
                 "Perform Quality Control checks on a phenotypes bundle file")))
+        parser.add_argument(
+            "--working-dir",
+            default=f"{tempfile.gettempdir()}/phenotypes_qc",
+            help=("The directory where this script will put its intermediate "
+                  "files."),
+            type=Path)
         return parser.parse_args()
 
     _logger = getLogger("phenotypes_qc")
-- 
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