From 21dcae967223f029f266886220f735b7859d2b8e Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 13 Jan 2019 16:01:09 -0600
Subject: [PATCH] Fix narrowpeak file name.
---
workflow/scripts/call_peaks_macs.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index b5170e2..69a5968 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -125,11 +125,12 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# MACS2 sometimes calls features off the end of chromosomes.
# Remove coordinates outside chromosome sizes
- narrowpeak_fn = '%s.narrowPeak' % (prefix)
+ int_narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
+ narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
- steps = ['slopBed -i %s -g %s -b 0' % (narrowpeak_fn, chrom_sizes),
+ steps = ['slopBed -i %s -g %s -b 0' % (int_narrowpeak_fn, chrom_sizes),
'bedClip stdin %s %s' % (chrom_sizes, clipped_narrowpeak_fn)]
out, err = utils.run_pipe(steps)
--
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