From 6a48dd58cf27325e560cef3d68ac2bc0431da83a Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Thu, 3 Feb 2022 13:44:56 +0100
Subject: [PATCH] Update runme.sh

---
 runme.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/runme.sh b/runme.sh
index 099b641..9344d47 100644
--- a/runme.sh
+++ b/runme.sh
@@ -15,6 +15,7 @@ conda install -c anaconda pandas
 conda install -c bioconda pysam
 
 #run the workflow:
+## DEPRECATED, follow the readme.md
 conda activate snakemake
 module load graalvm/ce-java8-20.0.0 fastqc
 module load samtools/1.10
@@ -28,8 +29,7 @@ module load MultiQC/1.9
 
 sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --nolock
 
-
-# or without module: 
+#run the workflow without loading modules before (with --use-envmodules): 
 conda activate snakemake
 #check the pipeline:
 snakemake --use-envmodules -n
-- 
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