cluster.json~

{
    "__default__" :
    {
        "mem" : "32g",
        "time" : "96:00:00",
        "partition" : "ccr",
        "threads": "1",
        "gres":"lscratch:256"
    },
    "bicseq":
    {
        "threads": "1"
    },
    "bwa_pe":
    {
        "threads": "4"
    },
    "bwa.mem":
    {
        "mem": "128g",
        "threads": "8"
    },

    "fastqc_fastq":
    {
        "threads": "8"
    },
    "fastqc_trimmed":
    {
        "threads": "8"
    },
    "gatk_apply_variant_recal":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_apply_vqsr":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_combine_gvcfs":
    {
        "threads": "1",
        "time" : "48:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs":
    {
        "threads": "6",
        "time" : "96:00:00",
        "mem": "96g"
    },
    "gatk_genotyping":
    {
        "threads": "1",
    },
    "gatk_haplotype_caller":
    {
        "threads": "8",
        "mem": "64g"
    },
    "gatk_realign":
    {
        "threads": "1",
        "gres":"lscratch:500",
        "mem": "64g"
    },
    "gatk_recal":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_variant_annnotator":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_variant_recal":
    {
        "threads": "1",
        "mem": "64g"
    },
    "ngsqc":
    {
        "threads": "1"
    },
    "novocraft_novoalign":
    {
        "threads": "16"
    },
    "novocraft_sort":
    {
        "threads": "1",
        "mem": "64g"
    },
    "novo_sort":
    {
        "threads": "1",
        "mem": "64g"
    },
    "picard_headers2":
    {
        "threads": "1"
    },
    "picard_index_bam":
    {
        "threads": "1",
        "time": "01:00:00"
    },
    "picard_headers":
    {
        "threads": "1"
    },
    "picard_markdups":
    {
        "threads": "1"
    },
    "qualimap":
    {
        "threads": "8",
        "mem": "96g"
    },
    "samtools_flagstats_dedup":
    {
        "threads": "1"
    },
    "samtools_flagstats":
    {
        "threads": "1"
    },
    "samtools_mpileup":
    {
        "threads": "1"
    },
    "samtools_sam2bam":
    {
        "threads": "1"
    },
    "samtools_sort":
    {
        "threads": "1"
    },
    "script_batchgvcf":
    {
        "threads": "1"
    },
    "script_bzip2":
    {
        "threads": "1"
    },
    "script_checkqc":
    {
        "threads": "1"
    },
    "script_coverage_qc":
    {
        "threads": "1"
    },
    "script_split_gvcfs":
    {
        "threads": "1"
    },
    "snpeff_dbnsfp":
    {
        "threads": "1"
    },
    "snpeff":
    {
        "threads": "1"
    },
    "star_align_2":
    {
        "threads": "8"
    },
    "star_align":
    {
        "threads": "8"
    },
    "star_generate":
    {
        "threads": "1"
    },
    "trimmomatic":
    {
        "threads": "4"
    },
    "varscan":
    {
        "threads": "1"
    }
}