From bd2e9a4dc3470b9e8b011c4c32413d4766b280ca Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 15 Jul 2024 12:37:37 +0200
Subject: [PATCH] Wrong variable name.
---
singularity/run_pipeline.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/singularity/run_pipeline.sh b/singularity/run_pipeline.sh
index 32bff4d..c3485ce 100755
--- a/singularity/run_pipeline.sh
+++ b/singularity/run_pipeline.sh
@@ -110,7 +110,7 @@ fi
[[ ${QOS} ]] || QOS="normal"
[[ ${PART} ]] || PART="common"
-batch_cmd="sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} ${wrapper} ${container}"
+sbatch_cmd="sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} ${wrapper} ${container}"
cluster_opts="--cluster \'${sbatch_cmd}\' --cluster-config ${cluster_config}"
#cluster_opts="--cores 20 --cluster \'sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} --mpi=none\' -j 300"
#cmd="APPTAINERENV_USER=${USER} apptainer run --cleanenv -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} ${pipeline_config} ${cluster_opts} --cluster-config ${cluster_config}"
--
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