From 6e343c4d05f1adcd6450685408ea714b5407d33b Mon Sep 17 00:00:00 2001
From: Susheel Busi <susheel.busi@uni.lu>
Date: Fri, 29 May 2020 15:13:08 +0200
Subject: [PATCH] Update ANALYSIS_RULES
---
2019_GDB/rules/ANALYSIS_RULES | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/2019_GDB/rules/ANALYSIS_RULES b/2019_GDB/rules/ANALYSIS_RULES
index 4da7df8..d33fe5f 100755
--- a/2019_GDB/rules/ANALYSIS_RULES
+++ b/2019_GDB/rules/ANALYSIS_RULES
@@ -183,7 +183,8 @@ rule minced:
shell:
"""
(date &&\
- ./minced {input} {output.mn1} {output.mn2} &&\
+ export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/ &&\
+ minced {input} {output.mn1} {output.mn2} &&\
echo $(basename -s "" {output.mn1}) >> minced_CRISPR_output.txt &&\
grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
date) &> >(tee {log})
--
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