From 91da721bea6942d7851409db9765d2853d272237 Mon Sep 17 00:00:00 2001
From: root <root@EB10PA4.newcefe.newage.fr>
Date: Thu, 5 Dec 2019 13:57:48 +0100
Subject: [PATCH] add script optimal_pipeline
---
optimal_pipeline/optimal_pipeline.sh | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/optimal_pipeline/optimal_pipeline.sh b/optimal_pipeline/optimal_pipeline.sh
index c991417..d76f0a1 100644
--- a/optimal_pipeline/optimal_pipeline.sh
+++ b/optimal_pipeline/optimal_pipeline.sh
@@ -8,7 +8,7 @@
##
###############################################################################
## Usage:
-## bash obitools_reference/total_obitools.sh
+## bash optimal_pipeline/optimal_pipeline.sh
##
## Description:
## ..............
@@ -35,7 +35,7 @@ cutadapt=${SINGULARITY_EXEC_CMD}" "${EDNATOOLS_SIMG}" cutadapt"
# Prefix for all generated files
pref=grinder_teleo1
# Prefix of the final table
-step=merging_vsearch
+step=optimal_pipeline
# Path to forward and reverse fastq files
R1_fastq="${DATA_PATH}"/"$pref"/"$pref"_R1.fastq
R2_fastq="${DATA_PATH}"/"$pref"/"$pref"_R2.fastq
@@ -48,8 +48,8 @@ base_dir=${REFDB_PATH}
### Prefix of the ref database files must not contain "." ou "_"
base_pref=`ls $base_dir/*sdx | sed 's/_[0-9][0-9][0-9].sdx//g' | awk -F/ '{print $NF}' | uniq`
# Path to intermediate and final folders
-main_dir=`pwd`"/01_merging/Outputs/01_vsearch/main"
-fin_dir=`pwd`"/01_merging/Outputs/01_vsearch/final"
+main_dir=`pwd`"/optimal_pipeline/Outputs/main"
+fin_dir=`pwd`"/optimal_pipeline/Outputs/final"
###################################################################################################################
--
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