cluster_config.json

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

        "run_command_sge": "--drmaa=\" -cwd -V -l h_vmem={cluster.h_vmem}M -l h_rt={cluster.h_rt} -pe smp {cluster.pe} -j yes -o {cluster.output} -e {cluster.errors}\"",

        "run_command_slurm": "--drmaa=\" --mem-per-cpu={cluster.h_vmem} -t {cluster.h_rt} -c {cluster.pe} -p medium -o {cluster.output} -e {cluster.errors}\""
    },
    
    "__default__":
    {
        "output": "cluster_log/{rule}.{jobid}.out",
        "errors": "cluster_log/{rule}.{jobid}.err",
        
        "h_vmem": "2000",
        "h_rt": "4:00:00",
        "pe": "4",
        "P":"medium"
    },

    "star":
    {
        "h_vmem": "20000",
        "h_rt": "40:00:00",
        "pe": "8"
    },

    "star_index":
    {
        "h_vmem": "20000",
        "h_rt": "40:00:00",
        "pe": "8"
    },

    "salmon":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "8"
    },

    "salmon_index":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "8"
    },

    "generate_transcriptome":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "8"
    },

    "feature_counts":
    {
        "h_vmem": "16000",
        "h_rt": "4:00:00",
        "pe": "2"
    },

    "infer_experiment":
    {
        "h_vmem": "2000",
        "h_rt": "4:00:00",
        "pe": "1"
    },

    "qualimap_rnaseq":
    {
        "h_vmem": "64000",
        "h_rt": "40:00:00",
        "pe": "1"
    },

    "qualimap_bamqc":
    {
        "h_vmem": "64000",
        "h_rt": "40:00:00",
        "pe": "1"
	},

    "dupradar":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "1"
    },

    "ciri":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "8"
    },
    
    "bwa":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "8"
    },
    
    "bwa_index":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "4"
    },

    "cellranger_count":
    {
        "h_vmem": "4000",
        "h_rt": "40:00:00",
        "pe": "1"
    },

    "velocyto_run":
    {
        "h_vmem": "20000",
        "h_rt": "40:00:00",
        "pe": "8"
    }
}