From 61d91caecad9df9a43cb389e5462a253d0e767c3 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 14 Aug 2019 17:33:00 +0200
Subject: [PATCH] Also generate bedgraph.
---
bigwig_average_over_bed/wrapper.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/bigwig_average_over_bed/wrapper.py b/bigwig_average_over_bed/wrapper.py
index 629effb..bb4f61f 100644
--- a/bigwig_average_over_bed/wrapper.py
+++ b/bigwig_average_over_bed/wrapper.py
@@ -3,7 +3,7 @@ from libworkflows import run_with_modules
load_modules = snakemake.config.get("load_modules", False)
if load_modules:
- modules = ["UCSC-tools/v373"]
+ modules = ["bioawk", "UCSC-tools/v373"]
else:
modules = []
@@ -14,7 +14,9 @@ bigWigAverageOverBed \\
{snakemake.params.genome_binned} \\
/dev/null \\
2> {snakemake.log.err}
+ bioawk -t '{{print $1,$2,$3,$5}}' {snakemake.output.bed} \\
+ 2>> {snakemake.log.err} \\
+ > {snakemake.output.bedgraph}
"""
-#run_with_modules(shell_commands, modules)
shell(run_with_modules(shell_commands, modules))
--
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