cluster.json

{
    "documenation": {
        "cmdline": "Use with snakemake -j 999 --cluster-config cluster.json --cluster 'sbatch --job-name {cluster.job-name} --ntasks-per-node {cluster.ntasks-per-node} --cpus-per-task {threads} --mem-per-cpu {cluster.mem-per-cpu} --partition {cluster.partition} --time {cluster.time} --mail-user {cluster.mail-user} --mail-type {cluster.mail-type} --error {cluster.error} --output {cluster.output}'"
    },
    "__default__": {
        "account": "kretzler",
        "job-name": "SM.{rule}",
        "partition": "standard",
        "nodes": "1",
        "time": "10:00:00",
        "ntasks-per-node": "1",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb",
        "output": "logs/%j.%N.out.txt",
        "error": "logs/%j.%N.err.txt",
        "mail-user": "$USER@umich.edu",
        "mail-type": "ALL"
    },
    "HtSeq_Count": {
        "mem-per-cpu": "4gb",
        "time": "10:00:00"
    },
    "fastqScreen": {
        "mem-per-cpu": "16gb",
        "time": "2:00:00"
    },
    "fastqc": {
        "mem-per-cpu": "1gb",
        "time": "00:45:00"
    },
    "STAR_fq": {
        "time": "10:00:00",
        "cpus-per-task": "12",
        "mem-per-cpu": "14gb"
    },
    "StringTie": {
        "time": "01:00:00",
        "cpus-per-task": "6",
        "mem-per-cpu": "16gb"
    },
    "Picard": {
        "time": "01:00:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "8gb"
    },
    "HtSeqPca": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    },
    "BallGownGenePca": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    },
    "BallGownTxPca": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    },
    "HtSeqCluster": {
        "time": "10:00:00",
        "cpus-per-task": "12",
        "mem-per-cpu": "4gb"
    },
    "BallGownGeneCluster": {
        "time": "10:00:00",
        "cpus-per-task": "12",
        "mem-per-cpu": "4gb"
    },
    "BallGwownTxCluster": {
        "time": "10:00:00",
        "cpus-per-task": "12",
        "mem-per-cpu": "12gb"
    },
    "HtSeqBoxPlot": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    },
    "BallGownGeneBoxPlot": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    },
    "BallGownTcBoxPlot": {
        "time": "00:30:00",
        "cpus-per-task": "1",
        "mem-per-cpu": "4gb"
    }
}