Commit 8e447c31 authored by Holly Ruess's avatar Holly Ruess

fix input error

parent 6e63a569
Pipeline #7067 canceled with stages
in 414 minutes and 18 seconds
......@@ -182,12 +182,13 @@ def blacklist_peaks(experiment, blacklist):
logger.info("Removing blacklist regions from replicated peaks")
narrowpead_input = "%s.replicated.narrowPeak" % (experiment)
# Assign output
blpo_filename = "%s.replicated_noblacklist.narrowPeak" % (experiment)
# Remove
steps = [
"bedtools intersect -v -a %s -b %s" % (experiment, blacklist),
"bedtools intersect -v -a %s -b %s" % (narrowpead_input, blacklist),
r"""awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}'""",
]
out, err = utils.run_pipe(steps, blpo_filename)
......
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