From 21aac926c868a888f68db3428d165ce04ea2d766 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 14 Jan 2019 15:46:18 -0600
Subject: [PATCH] Fix output directories and file names.
---
workflow/main.nf | 1 +
workflow/scripts/call_peaks_macs.py | 1 +
2 files changed, 2 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index 6b59b77..4e9c50d 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -369,6 +369,7 @@ peaksDesign = experimentPeaks
process consensusPeaks {
publishDir "$outDir/${task.process}", mode: 'copy'
+ publishDir "$outDir/design", mode: 'copy', pattern: '*.{csv|tsv}'
input:
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 99e2900..17b1414 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -239,6 +239,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Remove temporary files
os.remove(clipped_narrowpeak_fn)
os.remove(rescaled_narrowpeak_fn)
+ os.remove(int_narrowpeak_fn)
def main():
--
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