From 86c8bd50525ab7fcfb355f86dd282ac143d9ef30 Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Mon, 13 Apr 2015 15:40:31 +0200
Subject: [PATCH] fix #20
---
rules/Analysis/MGMT.rules | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/rules/Analysis/MGMT.rules b/rules/Analysis/MGMT.rules
index bebfbd3..a4207d1 100644
--- a/rules/Analysis/MGMT.rules
+++ b/rules/Analysis/MGMT.rules
@@ -11,7 +11,7 @@ rule ANALYSIS_ANNOTATE:
"%s/annotation/annotation.filt.gff" % AN_OUT
shell:
"""
- prokka --force --outdir {AN_OUT}/annotation --cpus {THREADS} --metagenome --norrna {input[0]} > {log} 2>&1
+ prokka --force --outdir {AN_OUT}/annotation --cpus {THREADS} --metagenome --norrna {input[0]} >> {log} 2>&1
# Prokka gives a weird gff file with all the sequences. We need to write some small code to produce a file that
# cleans up the output
@@ -159,7 +159,7 @@ rule ANALYSIS_MG_VARIANT_CALLING:
# Clean up directory
echo "Cleaning up directory"
- cat log.txt > {log}
+ cat log.txt >> {log}
rm -f {AN_OUT}/MG.variants.isec.vcf log.txt
"""
@@ -226,7 +226,7 @@ rule ANALYSIS_MT_VARIANT_CALLING:
# Clean up directory
echo "Cleaning up directory"
- cat log.txt > {log}
+ cat log.txt >> {log}
rm -f {AN_OUT}/MT.variants.isec.vcf log.txt
"""
--
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