cluster_config_slurm.json

{
    "__set_run_command__":
    {
        "snake_opt": "-j 100 -k --restart-times 0 --max-jobs-per-second 5 --rerun-incomplete",

        "run_command": "--profile \"cubi-dev\""
    },
    
    "__default__":
    {
        "output": "cluster_log/{rule}.{jobid}.out",
        "error": "cluster_log/{rule}.{jobid}.err",
        
        "mem": "2000M",
        "time": "4:00:00",
        "cpus-per-task": 4,
        "partition":"medium"
    },

    "star":
    {
        "mem": "60000M",
        "time": "8:00:00",
        "cpus-per-task": 8
    },

    "star_index":
    {
        "mem": "40000M",
        "time": "8:00:00",
        "cpus-per-task": 8
    },

    "salmon":
    {
        "mem": "32000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },

    "salmon_index":
    {
        "mem": "96000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },

    "generate_transcriptome":
    {
        "mem": "32000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },

    "feature_counts":
    {
        "mem": "16000M",
        "time": "4:00:00",
        "cpus-per-task": 2
    },

    "infer_experiment":
    {
        "mem": "2000M",
        "time": "4:00:00",
        "cpus-per-task": 1
    },

    "qualimap_rnaseq":
    {
        "mem": "64000M",
        "time": "40:00:00",
        "cpus-per-task": 1
    },

    "qualimap_bamqc":
    {
        "mem": "64000M",
        "time": "40:00:00",
        "cpus-per-task": 1
	},

    "dupradar":
    {
        "mem": "4000M",
        "time": "40:00:00",
        "cpus-per-task": 1
    },

    "ciri":
    {
        "mem": "4000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },
    
    "bwa":
    {
        "mem": "4000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },
    
    "bwa_index":
    {
        "mem": "4000M",
        "time": "40:00:00",
        "cpus-per-task": 4
    },

    "cellranger_count":
    {
        "mem": "4000M",
        "time": "40:00:00",
        "cpus-per-task": 1
    },

    "velocyto_run":
    {
        "mem": "20000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },
    "preseq_lc_extrap":
    {
        "mem": "40000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },
    "preseq_c_curve":
    {
        "mem": "40000M",
        "time": "40:00:00",
        "cpus-per-task": 8
    },
    "tmod_dbs":
    {
        "mem": "16000M",
        "time": "8:00:00",
        "cpus-per-task": 8
    },

    "cluster_profiler":
    {
        "mem": "8000M",
        "time": "4:00:00",
        "cpus-per-task": 8
    }


}