Remove temporary files.

metagenopolis · Sep 2, 2024 · 6ff0703 · 6ff0703
1 parent 582c3bf
commit 6ff0703
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/meteor/variantcalling.py b/meteor/variantcalling.py
@@ -500,6 +500,8 @@ def execute(self) -> None:
             # Ensure the temporary file is removed after use
             if os.path.isfile(temp_ref_file_path):
                 os.remove(temp_ref_file_path)
+            if os.path.isfile(temp_ref_file_path + ".fai"):
+                os.remove(temp_ref_file_path + ".fai")
         logging.info(
             "Completed freebayes step in %f seconds", perf_counter() - startfreebayes
         )
@@ -543,3 +545,5 @@ def execute(self) -> None:
             cram_file, vcf_file, consensus_file, freebayes_version
         )
         self.save_config(config, self.census["Stage3FileName"])
+        if os.path.isfile(temp_bed_file.name):
+            os.remove(temp_bed_file.name)