From e98663edc1ada810a23692bcef1f87ab619a652e Mon Sep 17 00:00:00 2001
From: "Susheel Bhanu Busi susheel.busi@uni.lu" <susheel.busi@uni.lu>
Date: Sat, 30 May 2020 14:53:58 +0200
Subject: [PATCH] fixed the path for the minced_CRISPR_output.txt file, and
also fixed the CASC issue
---
2019_GDB/rules/ANALYSIS_RULES | 4 ++--
rules/ANALYSIS_RULES | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/2019_GDB/rules/ANALYSIS_RULES b/2019_GDB/rules/ANALYSIS_RULES
index 105255a..d1eb573 100755
--- a/2019_GDB/rules/ANALYSIS_RULES
+++ b/2019_GDB/rules/ANALYSIS_RULES
@@ -187,8 +187,8 @@ rule minced:
(date &&\
export PATH={config[minced][PATH]} &&\
minced {input} {output.mn1} {output.mn2} &&\
- echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
- grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
+ echo $(basename -s ".txt" {output.mn1}) >> analysis/crispr/minced/minced_CRISPR_output.txt &&\
+ grep -c 'CRISPR' {output.mn1} >> analysis/crispr/minced/minced_CRISPR_output.txt &&\
date) &> >(tee {log})
"""
diff --git a/rules/ANALYSIS_RULES b/rules/ANALYSIS_RULES
index 105255a..d1eb573 100755
--- a/rules/ANALYSIS_RULES
+++ b/rules/ANALYSIS_RULES
@@ -187,8 +187,8 @@ rule minced:
(date &&\
export PATH={config[minced][PATH]} &&\
minced {input} {output.mn1} {output.mn2} &&\
- echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
- grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
+ echo $(basename -s ".txt" {output.mn1}) >> analysis/crispr/minced/minced_CRISPR_output.txt &&\
+ grep -c 'CRISPR' {output.mn1} >> analysis/crispr/minced/minced_CRISPR_output.txt &&\
date) &> >(tee {log})
"""
--
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