Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in / Register
Toggle navigation
Menu
Open sidebar
BICF
Astrocyte
atacseq_analysis
Commits
8e447c31
Commit
8e447c31
authored
Jun 03, 2020
by
Holly Ruess
Browse files
fix input error
parent
6e63a569
Pipeline
#7067
canceled with stages
in 414 minutes and 18 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
workflow/scripts/overlap_peaks.py
View file @
8e447c31
...
...
@@ -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"
%
(
experimen
t
,
blacklist
),
"bedtools intersect -v -a %s -b %s"
%
(
narrowpead_inpu
t
,
blacklist
),
r
"""awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}'"""
,
]
out
,
err
=
utils
.
run_pipe
(
steps
,
blpo_filename
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment