cluster.json

{
    "__default__" :
    {
        "mem" : "64g",
        "time" : "96:00:00",
        "partition" : "ccr,norm",
        "threads": "4",
        "gres":"lscratch:256"
    },
    "bicseq":
    {
        "threads": "1"
    },
    "theta":
    {
        "threads": "1",
        "mem" : "48g"
    },
    "manta_germline":
     {
        "threads": "8",
        "mem" : "96g",
    },
    "cnvkit_somatic":
     {
        "threads": "1",
        "mem" : "48g",
    },
    "manta_somatic":
     {
        "threads": "8",
        "mem" : "96g",
    },
    "manta_wgs":
    {
        "threads": "8",
        "mem" : "96g",
    },
    "conpair":
    {
        "threads": "1"
    },
    "make_germline_network":
    {
        "threads": "1",
        "mem" : "64g",
    },
    "avia_make_bed_germ":
    {
        "mem" : "96g"
    },
    "make_somatic_network":
    {
        "threads": "1",
        "mem" : "64g",
    },
    "somatic_germline_calls":
    {
        "threads": "4",
        "mem" : "64g"
    },
    "multiqc":
    {
        "threads": "1"
    },
    "fastq_screen":
    {
        "threads": "24"
    },
    "strelka":
    {
        "threads": "4",
        "mem": "64g"
    },
    "bwa_pe":
    {
        "threads": "4"
    },
    "bwa_mem":
    {
        "mem": "48g",
        "threads": "32"
    },
    "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" : "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": "120g"
    },
    "gatk_genotype_somatic_gvcfs":
    {
        "threads": "4",
        "time" : "10-00:00:00",
        "mem": "120g"
    },
    "gatk_splitcigar":
    {
        "threads": "1",
        "mem": "96g"
    },
    "gatk_genotyping":
    {
        "threads": "1",
    },
    "gatk_haplotype_caller":
    {
        "threads": "4",
        "mem": "64g"
    },
    "gatk_realign":
    {
        "threads": "1",
        "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": "96g"
    },
    "qualimap_rna":
    {
        "threads": "8",
        "mem": "96g"
    },
    "qualimap_wgs":
    {
        "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",
        "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" : "64g"
    },
    "star_align_1":
    {
        "threads": "32",
        "mem" : "64g"
    },
    "germline_filter_rnaseqvar":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_select_variants_rnaseqvar":
    {
        "threads": "1",
        "mem": "64g"
    },
    "gatk_rnaseqvar_haplotype_caller":
    {
        "threads": "4",
        "mem": "48g"
    },
    "star_generate":
    {
        "threads": "1"
    },
    "trimmomatic":
    {
        "threads": "32"
    },
    "varscan":
    {
        "threads": "1"
    },
    "gatk_chrom_mutect2":
    {
        "time": "6-00:00:00",
        "threads": "2"
    },
    "gatk_mutect2":
    {
        "time": "10-00:00:00",
        "threads": "2",
        "mem": "120g"
    },
    "trimmomatic_pe":
    {
        "threads": "32",
        "mem": "110g"
    },
    "fastqc":
    {
        "threads": "32",
        "mem": "110g"
    },
    "star1p":
    {
        "threads": "32",
        "mem": "110g"
    },
    "star2p":
    {
        "threads": "32",
        "mem": "110g"
    },
    "rsem":
    {
        "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"
    },
    

}