From e1f7f61b9795ed8482918757ec3088cc7e1f9734 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 6 Jan 2019 21:14:55 -0600
Subject: [PATCH] Add summits and remove extra names in files.
---
workflow/main.nf | 1 +
workflow/scripts/call_peaks_macs.py | 2 +-
workflow/tests/test_call_peaks_macs.py | 6 ++++--
3 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 3bd2edf..ac29389 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -342,6 +342,7 @@ process callPeaksMACS {
output:
set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks
+ file '*.xls' into summit
script:
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 23174e0..28c546c 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -125,7 +125,7 @@ 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_peaks.narrowPeak' % (prefix)
+ narrowpeak_fn = '%s.narrowPeak' % (prefix)
clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index 71358bc..dabfd71 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -12,7 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
def test_call_peaks_macs_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
- peak_file = test_output_path + 'ENCLB144FDT_peaks.narrowPeak'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.xls'))
+ peak_file = test_output_path + 'ENCLB144FDT.narrowPeak'
assert utils.count_lines(peak_file) == 227389
@@ -20,5 +21,6 @@ def test_call_peaks_macs_singleend():
def test_call_peaks_macs_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
- peak_file = test_output_path + 'ENCLB568IYX_peaks.narrowPeak'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls'))
+ peak_file = test_output_path + 'ENCLB568IYX.narrowPeak'
assert utils.count_lines(peak_file) == 112652
--
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