Allocate GRES with fastqc lscratch tmp directory

OpenOmics · Mar 8, 2024 · 95a5d9a · 95a5d9a
1 parent 7e8211e
commit 95a5d9a
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/config/cluster.json b/config/cluster.json
@@ -2,7 +2,8 @@
     "__default__": {
         "threads": "4",
         "mem": "16g",
-        "time": "0-04:00:00"
+        "time": "0-04:00:00",
+        "gres": "lscratch:64"
     },
     "fastp": {
         "threads": "8",

diff --git a/src/run.sh b/src/run.sh
@@ -192,7 +192,7 @@ function submit(){
           # --keep-remote --restart-times 3 -j 500 --use-singularity 
           # --singularity-args -B {}.format({bindpaths}) --local-cores 24
           SLURM_DIR="$3/logfiles/slurmfiles"
-          CLUSTER_OPTS="sbatch --cpus-per-task {cluster.threads} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
+          CLUSTER_OPTS="sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
           # Check if NOT running on Biowulf
           # Assumes other clusters do NOT 
           # have GRES for local node disk,