diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py index 8c090aee9774f9925118b8a062a799e73dfc8c5a..e091296b50b04635b6bfef68ec51dd110b96c886 100644 --- a/workflow/scripts/convert_reads.py +++ b/workflow/scripts/convert_reads.py @@ -30,7 +30,7 @@ def get_args(): formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('-b', '--bam', - help="The bam file to run filtering and qc on.", + help="The bam file to convert.", required=True) parser.add_argument('-p', '--paired', @@ -116,7 +116,7 @@ def main(): convert_mapped_pe(bam, bam_basename) else: bedse_filename = bam_basename + ".bedse.gz" - shutil(tag_filename, bedse_filename) + shutil.copy(tag_filename, bedse_filename) if __name__ == '__main__':