diff --git a/genie/process_mutation.py b/genie/process_mutation.py index d6d31d29..6021b944 100644 --- a/genie/process_mutation.py +++ b/genie/process_mutation.py @@ -250,6 +250,7 @@ def annotate_mutation( """ input_files_dir = tempfile.mkdtemp(dir=workdir) output_files_dir = tempfile.mkdtemp(dir=workdir) + error_dir = os.path.join(output_files_dir, f"{center}_error_reports") for mutation_file in mutation_files: move_mutation(mutation_file, input_files_dir) @@ -262,6 +263,7 @@ def annotate_mutation( os.path.join(genie_annotation_pkg, "annotation_suite_wrapper.sh"), f"-i={input_files_dir}", f"-o={output_files_dir}", + f"-e={error_dir}", f"-m={merged_maf_path}", f"-c={center}", "-s=WXS",