cluster.json

{
    "__default__" :
    {
        "queue"     : "normal",
        "nCPUs"     : "1",
        "memory_R"  : "rusage[mem=2000]",
        "memory_M"  : "2000000",
        "name"      : "JOBNAME.{rule}.{wildcards}",
        "output"    : "logs/{rule}.{wildcards}.out",
        "error"     : "logs/{rule}.{wildcards}.err",
        "hosts"     :  "span[hosts=1]",
        "n_cores"   :  1
    },


    "assemble_genome_corrected_paired_reads_with_spades" :
    {
        "memory_R"    : "rusage[mem=16000]",
        "memory_M"    : "16000000",
        "n_cores"     :  4
    },


    "determine_mlst_from_trimmed_reads" :
    {
        "memory_R"    : "rusage[mem=4000]",
        "memory_M"    : "4000000",
        "n_cores"     :  4
    },

    "correct_error_paired_reads_with_spades" :
    {
        "memory_R"    : "rusage[mem=16000]",
        "memory_M"    : "16000000",
        "n_cores"     :  4
    },

    "remove_duplicates_from_mapping" :
    {
        "memory_R"    : "rusage[mem=10000]",
        "memory_M"    : "10000000",
        "n_cores"     :  1

    },

    "genotype_with_freebayes_on_all_samples" :
    {
        "memory_R"     :  "rusage[mem=16000]",
        "memory_M"     :  "16000000",
        "n_cores"      :  4,
        "queue"        :  "long"
    },

    "genotype_with_HaplotypeCaller_GATK_BP_RESOLUTION" :
    {
        "memory_R"     :  "rusage[mem=8000]",
	      "memory_M"     :  "8000000"
    },
     "merge_gvcf_files_with_CombineGVCFs_GATK":
    {
        "memory_R"     :  "rusage[mem=16000]",
      	"memory_M"     :  "16000000"
    }
}