cluster.json

{
    "__default__" :
    {
        "mem" : "48g",
        "time" : "96:00:00",
        "partition" : "ccr,norm",
        "threads": "4",
        "gres":"lscratch:256"
    },
    "trim_pe":
    {
        "threads": "32",
        "mem": "24g"
    },
    "trim_se":
    {
        "threads": "32",
        "mem": "24g"
    },
    "stats":
    {
        "mem": "110g",
        "threads": "4",
        "gres":"lscratch:256"
    },    
    "picard":
    {
        "mem": "110g",
        "gres":"lscratch:256",
        "threads":"2"
    },    
    "picard_dedup":
    {
        "mem": "110g",
        "gres":"lscratch:256",
        "threads":"2"
    },    
    "rawfastqc":
    {
        "threads": "8",
    },    
    "fastqc":
    {
        "threads": "8",
    },
    "deeptools_prep":
    {
        "mem": "4g",
        "threads": "2",
    },
    "deeptools":
    {
        "mem": "24g",
    },
    "ppqt":
    {
        "mem": "24g"
    },
    "preseq":
    {
        "mem": "24g"
    },
    "dedup":
    {
        "mem": "24g"
    },
    "ngsplot":
    {
        "mem": "24g"
    },
    "bicseq":
    {
        "threads": "1"
    },
    "fusioncatcher":
    {
        "threads": "16",
        "mem" : "96g",
        "time" : "10-00:00:00",
    },
    "fusion_summary":
    {
        "threads": "1",
        "mem" : "12g",
        "time" : "1-00:00:00",
    },
    "rnafusioncleanup":
    {
        "threads": "1",
        "mem" : "12g",
        "time" : "1-00:00:00",
    },
    "canvas_wgs_germ":
    {
        "threads": "32",
        "mem" : "120g",
        "time" : "10-00:00:00",
    },
    "canvas_wgs_somatic":
    {
        "threads": "32",
        "mem" : "120g",
        "time" : "10-00:00:00",
    },
    "canvas_wgs_tumoronly":
    {
        "threads": "32",
        "mem" : "120g",
        "time" : "10-00:00:00",
    },
    "admixture_germline":
    {
        "threads": "32",
        "mem" : "96g",
        "time" : "5-00:00:00",
    },
    "admixture_somatic":
    {
        "threads": "32",
        "mem" : "96g",
        "time" : "5-00:00:00",
    },
    "admixture_wgs":
    {
        "threads": "32",
        "mem" : "96g",
        "time" : "5-00:00:00",
    },
    "admixture_wgs_somatic":
    {
        "threads": "32",
        "mem" : "96g",
        "time" : "5-00:00:00",
    },
    "svaba_germline":
    {
        "threads": "32",
        "mem" : "96g",
        "time" : "10-00:00:00",
    },
    "starfusion":
    {
        "threads": "1",
        "mem" : "48g",
        "time" : "10-00:00:00",
    },
    "vcf2maf_tumoronly":
    {
        "threads": "2",
        "mem" : "96g",
        "time" : "1-00:00:00",
    },
    "vcf2maf_mutect":
    {
        "threads": "2",
        "mem" : "96g",
        "time" : "1-00:00:00",
    },
    "vcf2maf_mutect2":
    {
        "threads": "2",
        "mem" : "96g",
        "time" : "1-00:00:00",
    },
    "vcf2maf_strelka":
    {
        "threads": "2",
        "mem" : "96g",
        "time" : "1-00:00:00",
    },
    "fusioninspector":
    {
        "threads": "1",
        "mem" : "48g",
    },
    "oncofuse":
    {
        "threads": "1",
        "mem" : "48g",
    },
    "theta":
    {
        "threads": "1",
        "mem" : "48g",
        "time" : "10-00:00:00",
    },
    "wgs_theta":
    {
        "threads": "1",
        "mem" : "48g",
        "time" : "10-00:00:00",
    },
    "manta_germline":
     {
        "threads": "8",
        "mem" : "96g",
        "time" : "10-00:00:00",
    },
    "cnvkit_somatic":
     {
        "threads": "2",
        "mem" : "96g",
    },
    "cnvkit_wgs_somatic":
     {
        "threads": "2",
        "mem" : "96g",
    },
    "cnvkit_somatic_tumoronly":
     {
        "threads": "1",
        "mem" : "48g",
    },
    "cnvkit_germ":
     {
        "threads": "12",
        "mem" : "64g",
    },
    "manta_somatic":
     {
        "threads": "8",
        "mem" : "96g",
        "time" : "10-00:00:00",
    },
    "manta_wgs":
    {
        "threads": "8",
        "mem" : "96g",
        "time" : "10-00:00:00",
    },
    "conpair":
    {
        "threads": "1"
    },
    "make_germline_network":
    {
        "threads": "1",
        "mem" : "64g",
    },
    "avia_make_bed_germ":
    {
        "mem" : "96g"
    },
    "delly_germline":
    {
        "threads": "1",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic":
    {
        "threads": "1",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic_del":
    {
        "threads": "8",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic_ins":
    {
        "threads": "8",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic_dup":
    {
        "threads": "8",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic_trans":
    {
        "threads": "8",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "delly_somatic_inv":
    {
        "threads": "8",
        "mem" : "64g",
        "time" : "10-00:00:00",
    },
    "pindel_germline":
    {
        "threads": "8",
        "mem" : "64g",
    },
    "breakdancer_germline":
    {
        "threads": "1",
        "mem" : "64g",
    },
    "make_somatic_network":
    {
        "threads": "1",
        "mem" : "64g",
    },
    "somatic_germline_calls":
    {
        "threads": "4",
        "mem" : "64g"
    },
    "multiqc":
    {
        "threads": "2",
        "mem" : "24g"
    },
    "fastq_screen":
    {
        "threads": "24",
        "mem": "24g"
    },
    "strelka":
    {
        "threads": "4",
        "mem": "64g"
    },
        
       
    "bwa_pe":
    {
        "threads": "4"
    },
    "bwa_mem":
    {
        "mem": "48g",
        "threads": "32"
    },
    "fastqc_fastq":
    {
        "threads": "8",
        "mem": "24g"
    },
    "fastqc_rnaseqvar":
    {
        "threads": "8",
        "mem": "24g"
    },
    "fastqc_trimmed":
    {
        "threads": "8",
        "mem": "24g"
    },
    "gatk_apply_variant_recal":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_apply_vqsr":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_combine_gvcfs":
    {
        "threads": "1",
        "time" : "5-00:00:00",
        "mem": "96g"
    },
    "gatk_combine_somatic_gvcfs":
    {
        "threads": "1",
        "time" : "5-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_1":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_2":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_3":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_4":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_5":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_6":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_7":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_8":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_9":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_10":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_11":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_12":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_13":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_14":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_15":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_16":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_17":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_18":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_19":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_20":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_21":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_22":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_X":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_Y":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_gvcfs_MT":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_genotype_somatic_gvcfs":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "96g"
    },
    "gatk_splitcigar":
    {
        "threads": "1",
        "mem": "96g"
    },
    "gatk_genotyping":
    {
        "threads": "1",
    },
    "gatk_haplotype_caller":
    {
        "threads": "4",
        "mem": "64g",
        "time" : "10-00:00:00",
    },
    "gatk_realign":
    {
        "threads": "2",
        "gres":"lscratch:500",
        "mem": "64g"
    },
    "gatk_recal":
    {
        "threads": "32",
        "mem": "64g"
    },
    "gatk_variant_annnotator":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_variant_recal":
    {
        "threads": "1",
        "mem": "64g"
    },
    "ngsqc":
    {
        "threads": "1"
    },
    "novocraft_novoalign":
    {
        "time" : "6-00:00:00",   
        "threads": "32"
    },
    "novocraft_sort":
    {
        "threads": "8",
        "mem": "120g"
    },
    "novo_sort":
    {
        "threads": "8",
        "mem": "120g"
    },
    "picard_headers2":
    {
        "threads": "1",
        "mem": "24g"
    },
    "picard_rnaseqvarheaders":
    {
        "threads": "1"
    },
    "picard_rnaseqvar_markdups":
    {
        "threads": "1"
    },
    "picard_index_bam":
    {
        "threads": "1",
        "time": "01:00:00"
    },
    "picard_headers":
    {
        "threads": "1"
    },
    "picard_markdups":
    {
        "threads": "12"
    },
    "qualimap":
    {
        "threads": "8",
        "mem": "48g"
    },
    "qualimap_rna":
    {
        "threads": "8",
        "mem": "48g"
    },
    "qualimap_wgs":
    {
        "threads": "8",
        "mem": "48g"
    },
    "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",
        "mem" : "12g"
    },
    "script_somatic_batchgvcf":
    {
        "threads": "1",
        "mem" : "12g"
    },
    "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": "32",
        "mem" : "96g"
    },
    "star_align_1":
    {
        "threads": "32",
        "mem" : "96g"
    },
    "germline_filter_rnaseqvar":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_select_variants_rnaseqvar":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_rnaseqvar_haplotype_caller":
    {
        "threads": "4",
        "mem": "96g",
        "time" : "10-00:00:00",
    },
    "star_generate":
    {
        "threads": "1"
    },
    "trim":
    {
        "threads": "16",
        "mem": "24g"
    },
    "trimmomatic":
    {
        "threads": "32",
        "mem": "24g"
    },
    "varscan":
    {
        "threads": "1"
    },
    "gatk_chrom_mutect2":
    {
        "time": "10-00:00:00",
        "threads": "2"
    },
    "gatk_mutect2":
    {
        "time": "10-00:00:00",
        "threads": "4",
        "mem": "48g"
    },
    "trimmomatic_pe":
    {
        "threads": "32",
        "mem": "24g"
    },
    "fastqc":
    {
        "threads": "32",
        "mem": "24g"
    },
    "star1p":
    {
        "threads": "32",
        "mem": "110g"
    },
    "star2p":
    {
        "threads": "32",
        "mem": "110g"
    },
    "rsem":
    {
        "gres":"lscratch:500",
        "threads": "16"
    },
    "subread":
    {
        "gres":"lscratch:500",
        "threads": "16"
    },
    "subreadoverlap":
    {
        "gres":"lscratch:500",
        "threads": "16"
    },
    "salmon":
    {
        "threads": "6",
        "mem": "110g"
    },
    "sleuth":
    {
        "threads": "4",
        "mem": "110g"
    },
    "EBSeq":
    {
        "threads": "4",
        "mem": "110g"
    },
    "mirseq_init":
    {
        "threads": "1",
        "mem": "16g"
    },
    "cutadapt":
    {
        "threads": "1",
        "mem": "32g"
    },
    "fastqc_pretrim":
    {
        "threads": "1",
        "mem": "16g"
    },
    "fastqc_posttrim":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirdeep2_mapper":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_make_bams":
    {
        "threads": "1",
        "mem": "32g"
    },
    "mirseq_make_bams_bwa":
    {
        "threads": "1",
        "mem": "32g"
    },
    "mirdeep2":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_variants":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_gencode_classification":
    {
        "threads": "1",
        "mem": "16g"
    },
    "expression_reports":
    {
        "threads": "1",
        "mem": "16g"
    },
    "differential_expression":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_summarize":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_main_document":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_miRspring_bowtie":
    {
        "threads": "1",
        "mem": "16g"
    },
    "mirseq_miRspring_bwa":
    {
        "threads": "1",
        "mem": "16g"
    },

    "mirseq_targetscan":
    {
        "threads": "1",
        "mem": "16g"
    },
    
    'BWA':
    {
        'mem': '64g',
        'threads': '32'
    },

    'trim_step4':
    {
        'threads': '16'
    },
        
        
    'MEMEChIP':
    {
        'mem': '64g',
        'threads': '32'
    },

    "cellranger":
    {
        "threads": "40",
        "mem": "110g"
    },
    "scrna_initial":
    {
        "partition" : "largemem",
        "threads": "32",
        "mem": "1000g"
    },
    "scrna_jackstraw":
    {
        "partition" : "largemem",
        "threads": "32",
        "mem": "1000g"
    },
    "scrna_cluster":
    {
        "partition" : "largemem",
        "threads": "32",
        "mem": "1000g"
    },
    "kraken_se":
    {
        "cpus-per-task": "24",
        "mem":'110g',
        "gres":"lscratch:256"
    },
    "kraken_pe":
    {
        "cpus-per-task": "24",
        "mem":'110g',
        "gres":"lscratch:256"
    },
    "bam2bw":
    {
        "threads":'32'
    }  
}