switches to using mem-per-cpu

configs/cluster_config.json

@@ -3,13 +3,13 @@
         "ntasks": 1,
         "partition": "express",
         "cpus-per-task": "{threads}",
-        "mem": "8G",
+        "mem-per-cpu": "8G",
         "jobname": "QuaC.{rule}.{jobid}",
         "output": "{RULE_LOGS_PATH}/{rule}-%j.log"
     },
     "qualimap_bamqc": {
         "partition": "short",
-        "mem": "{params.java_mem}"
+        "mem-per-cpu": "{params.java_mem}"
     },
     "picard_collect_multiple_metrics": {
         "partition": "short"
@@ -18,6 +18,6 @@
         "partition": "short"
     },
     "multiqc_aggregation_all_samples": {
-        "mem": "24G"
+        "mem-per-cpu": "24G"
     }
 }

src/run_quac.py

@@ -133,7 +133,7 @@ def create_snakemake_command(args, repo_path, mount_paths):
         f"--profile '{snakemake_profile_dir}'",
         f"--cluster-config '{args.cluster_config}'",
         "--cluster 'sbatch --ntasks {cluster.ntasks} --partition {cluster.partition}"
-        " --cpus-per-task {cluster.cpus-per-task} --mem {cluster.mem}"
+        " --cpus-per-task {cluster.cpus-per-task} --mem-per-cpu {cluster.mem-per-cpu}"
         " --job-name {cluster.jobname} --output {cluster.output} --parsable'",
     ]