diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py index 5e856d5cd8ec040076382ef7b4b41f1cf3abae2e..846fad07493fe2dc5f9c922c6edccdd096ddfda4 100644 --- a/workflow/scripts/convert_reads.py +++ b/workflow/scripts/convert_reads.py @@ -130,7 +130,7 @@ def tn5_shift_tagalign(tag_filename, shitfted_tag_filename): steps = [ "zcat -f %s" % (tag_filename), - r"""awk 'BEGIN{OFS="\t"}{{if ($6 == "+") {{$2 = $2 + 4}}; else if ($6 == "-") {{$3 = $3 - 5}} print $0}}'""", + r"""awk 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}'""", "gzip -nc"] out, err = utils.run_pipe(steps, outfile=shitfted_tag_filename)