cluster.json

{
    "__default__":
    {
        "partition" : "hbfraser,owners,hns,normal",
        "time" : "02:00:00",
        "mem" : "8G",
        "cpus" : "1",
        "jobname" : "{rule}.{wildcards}",
        "error" : "/scratch/users/paedugar/somaticMutationsProject/clusterFiles/{rule}.{wildcards}.err",
        "output" : "/scratch/users/paedugar/somaticMutationsProject/clusterFiles/{rule}.{wildcards}.out"
    },
    
    "test":
    {
        "time" : "01:00:05"
    },
    
    "check_fastqIntegrity":
    {
        "time" : "1:00:00"
    },
    
    "star_map":
    {
        "mem" : "40G",
        "time" : "10:00:00",
        "cpus" : "8"
    },
    
    "sort_bam":
    {
        "time" : "4:00:00",
        "mem" : "16G"
    },
    
    "organize_tissues":
    {
        "time" : "00:10:00",
        "mem" : "2G"
    },
    
    "create_mutationPileup":
    {
       "time" : "08:00:00",
       "mem" : "4G"
    },
    
    "eliminateGermline_correctContext":
    {
        "time" : "06:00:00"
    },
    
    "get_stranded_context_counts":
    {
        "time" : "04:00:00"
    },
    
    "create_coverageMaps":
    {
        "time" : "02:00:00",
        "mem" : "2G"
    },
    
    "merge_pileups":
    {
        "time" : "00:30:00"
    },
    
    
    "call_mutations":
    {
        "time" : "01:00:00",
        "mem":"4G"
    },
    
    "call_MutationSignatures":
    {
        "cpus" : "16",
        "mem" : "64G"
    },
    
    "run_signature_analyzer":
    {
        "mem" : "16G",
        "time" : "12:00:00"
    },
    
    "find_unbiasedNsignatures":
    {
        "cpus" : "16",
        "mem" : "64G",
        "time" : "48:00:00"
    },
    
    "run_signatures_NMF":
    {
        "cpus" : "8",
        "mem" : "16G",
        "time" : "48:00:00"
    },
    
    "run_dndscv":
    {
        "mem" : "16G",
        "time" : "2:00:00"
    },
    
    "plot_mutationsVsMetadata_biologicalCors":
    {
        "mem" : "16G",
        "time" : "4:00:00"
    },
    
    "process_bamForGatk":
    {
        "mem" : "4G",
        "time" : "30:00"
    },
    
    "run_gatk":
    {
        "mem" : "4G",
        "cpus" : "1",
        "time" : "2:00:00"
    },
    
    "run_gatkFilter":
    {
        "mem" : "4G",
        "time" : "15:00"
    },
    
    "eliminate_germline":
    {
        "mem" : "4G",
        "time" : "1:00:00"
    },
    
    "run_mutationSignatureGWAS":
    {
        "mem" : "4G",
        "time" : "4:00:00"
    },
    
    "do_GWAS":
    {
        "mem" : "4G",
        "time" : "6:00:00"
    },
    
    "get_closestExon":
    {
        "mem" : "4G",
        "time" : "15:00"
    },
    
    "get_mutationEnrichmentCancerDrivers":
    {
        "time" : "6:00:00"
    },
    
    "addFilters_mutationPileup":
    {
        "time" : "01:00:00",
        "mem" : "4G"
    },
    
    "perform_tSNE":
    {
        "time" : "03:00:00",
        "mem" : "32G"
    },
    
    "get_cosmic_mutations":
    {
        "time" : "00:30:00",
        "mem" : "4G"
    },
    
    "call_mutations_eliminate_PoN":
    {
        "time" : "00:10:00",
        "mem" : "4G"
    },
    
    "mutation_association_expression_targeted":
    {
        "time" : "08:00:00",
        "mem" : "8G"
    },
    
    "mutation_association_expression_targeted_create_expMat":
    {
        "mem" : "8G"
    },
    
    "mutation_association_expression_targeted_plot":
    {
        "time" : "08:00:00",
        "mem" : "16G"
    }, 
    
    "gwas_clonality":
    {
        "mem" : "8G",
        "time" : "12:00:00"
    },
    
    "gwas_selection":
    {
        "mem" : "8G",
        "time" : "12:00:00"
    },
    
    "create_tables":
    {
        "mem" : "8G",
        "time" : "1:00:00"
    }
    
}