From f29fa7fc91a354a49c80c12a9c6fecbdd5cbd1b8 Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Tue, 7 Sep 2021 10:34:40 +0200
Subject: [PATCH] Update runme.sh

---
 runme.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/runme.sh b/runme.sh
index c6b3ff6..099b641 100644
--- a/runme.sh
+++ b/runme.sh
@@ -35,3 +35,8 @@ conda activate snakemake
 snakemake --use-envmodules -n
 #run the pipeline
 sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --use-envmodules --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --nolock
+
+
+#re-run the pipeline at specific step
+sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --use-envmodules --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --nolock --forcerun multiqc
+
-- 
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