diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py index db9973c9683fca648ace7c5b0a77fe2a6e1a72a2..e33035f57f3ad2daf24cf471e5120cd9b96d8f28 100644 --- a/workflow/scripts/map_qc.py +++ b/workflow/scripts/map_qc.py @@ -159,7 +159,7 @@ def dedup_mapped(bam, bam_basename, paired): with open(dup_file_qc_filename, 'w') as fh: sambamba_markdup_command = ( "sambamba markdup -t %d %s %s %s" - % (cpu_count(), sambamba_parms, bam, tmp_dup_mark_filename) + % (cpu_count(), sambamba_params, bam, tmp_dup_mark_filename) ) logger.info(sambamba_markdup_command) subprocess.check_call(