diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py index eb805a8584feb6afc7f0370cde6512427af62571..400b9160c016adf0ed94c34934d621697ebd9b22 100644 --- a/workflow/scripts/convert_reads.py +++ b/workflow/scripts/convert_reads.py @@ -119,7 +119,7 @@ def convert_mapped_pe(bam, bam_basename, tag_filename, chrm): tag_steps = ["zcat -f %s" % (bedpe_filename)] tag_steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""]) if chrm: - tag_steps.extend["grep -v 'chrM'"] + tag_steps.extend(["grep -v 'chrM'"]) tag_steps.extend(['gzip -cn']) out, err = utils.run_pipe(tag_steps, outfile=tag_filename) os.remove(bedpe_filename)