mitoBench_pipeline-SLURM.json

{
    "__default__" :
    {
        "partition" : "short",
        "mem"       : "8000",
        "time"      : "0-02:00",
        "out"       : "cluster_logs/slurm.%j.out",
        "err"       : "cluster_logs/slurm.%j.err"
    },

    "prepare_fastq" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00",
    },

    "adapterremoval" :
    {
        "mem"       : "8000",
        "partition" : "medium",
        "time"      : "2-00:00",
    },

    "bwa_aln" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "bwa_sampe" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "bwa_samse" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "bam2snpAD" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "snpAD_estimation" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "snpAD_call" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "snpAD_vcf2fa" :
    {
        "mem"       : "2000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "namesort_norewrap" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "revert_bamrewrap" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "sort_norewrap" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "flagstat" :
    {
        "mem"       : "2000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "subsample_damageprofiler" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "mixemt" :
    {
        "mem"       : "12000",
        "partition" : "medium",
        "time"      : "1-00:00"
    },

    "contamMix_create_sequencePanel" :
    {
        "mem"       : "4000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "contamMix_align_against_consensus" :
    {
        "mem"       : "6000",
        "partition" : "short",
        "time"      : "0-02:00"
    },

    "contamMix_estimate" :
    {
        "mem"       : "4000",
        "partition" : "medium",
        "time"      : "1-00:00"
    }
}