cluster.json

{
    "__default__": {
        "gres": "lscratch:256",
        "mem": "48g",
        "partition": "norm",
        "threads": "4",
        "time": "4-00:00:00"
    },
    "admixture_germline": {
        "mem": "96g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "admixture_somatic": {
        "mem": "96g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "admixture_wgs": {
        "mem": "96g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "admixture_wgs_somatic": {
        "mem": "96g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "avia_make_bed_germ": {
        "mem": "96g",
        "time": "1-00:00:00"
    },
    "bam2bw_rnaseq_pe": {
        "mem": "40g",
        "threads": "4"
    },
    "bam2bw_rnaseq_se": {
        "mem": "40g",
        "threads": "2"
    },
    "bam2bw": {
        "threads": "32"
    },
    "bicseq": {
        "threads": "1"
    },
    "breakdancer_germline": {
        "mem": "64g",
        "threads": "1"
    },
    "BWA": {
        "mem": "64g",
        "threads": "32"
    },
    "BWA_SE": {
        "mem": "64g",
        "threads": "32"
    },
    "BWA_PE": {
        "mem": "64g",
        "threads": "32"
    },
    "bwa_mem": {
        "mem": "48g",
        "threads": "32",
        "time": "10-00:00:00"
    },
    "bwa_pe": {
        "threads": "4",
        "time": "10-00:00:00"
    },
    "canvas_wgs_germ": {
        "mem": "120g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "canvas_wgs_somatic": {
        "mem": "120g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "canvas_wgs_tumoronly": {
        "mem": "120g",
        "threads": "32",
        "time": "2-00:00:00"
    },
    "cellranger": {
        "mem": "110g",
        "threads": "40"
    },
    "cnvkit_germ": {
        "mem": "64g",
        "threads": "12",
        "time": "2-00:00:00"
    },
    "cnvkit_somatic": {
        "mem": "96g",
        "threads": "2",
        "time": "2-00:00:00"
    },
    "cnvkit_somatic_tumoronly": {
        "mem": "48g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "cnvkit_wgs_somatic": {
        "mem": "96g",
        "threads": "2",
        "time": "2-00:00:00"
    },
    "conpair": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "cutadapt": {
        "mem": "32g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "dedup": {
        "mem": "24g"
    },
    "deeptools": {
        "mem": "24g"
    },
    "deeptools_fingerprint": {
        "threads":"8"
    },
    "deeptools_fingerprint_Q5DD": {
        "threads":"8"
    },
    "deeptools_genes": {
        "threads":"16"
    },
    "deeptools_prep": {
        "mem": "4g",
        "threads": "2"
    },
    "delly_germline": {
        "mem": "64g",
        "threads": "1",
        "time": "10-00:00:00"
    },
    "delly_somatic": {
        "mem": "64g",
        "threads": "1",
        "time": "10-00:00:00"
    },
    "delly_somatic_del": {
        "mem": "64g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "delly_somatic_dup": {
        "mem": "64g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "delly_somatic_ins": {
        "mem": "64g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "delly_somatic_inv": {
        "mem": "64g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "delly_somatic_trans": {
        "mem": "64g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "diffbind": {
        "threads":"10"
    },
    "diffbind_bed": {
        "mem": "4g",
        "threads":"1"
    },
    "differential_expression": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "EBSeq": {
        "mem": "110g",
        "threads": "4",
        "time": "1-00:00:00"
    },
    "expression_reports": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "fastq_screen": {
        "mem": "90g",
        "threads": "36",
        "time": "2-00:00:00"
    },
    "fastqc": {
        "mem": "24g",
        "threads": "32",
        "time": "1-00:00:00"
    },
    "fastqc_fastq": {
        "mem": "24g",
        "threads": "8",
        "time": "1-00:00:00"
    },
    "fastqc_posttrim": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "fastqc_pretrim": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "fastqc_rnaseqvar": {
        "mem": "24g",
        "threads": "8",
        "time": "1-00:00:00"
    },
    "fastqc_trimmed": {
        "mem": "24g",
        "threads": "8",
        "time": "1-00:00:00"
    },
    "fusion_summary": {
        "mem": "12g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "fusioncatcher": {
        "mem": "96g",
        "threads": "16",
        "time": "5-00:00:00"
    },
    "fusioninspector": {
        "mem": "48g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "gatk_apply_variant_recal": {
        "mem": "64g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "gatk_apply_vqsr": {
        "mem": "64g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "gatk_chrom_mutect2": {
        "threads": "2",
        "time": "10-00:00:00"
    },
    "gatk_combine_gvcfs": {
        "mem": "96g",
        "threads": "1",
        "time": "5-00:00:00"
    },
    "gatk_combine_somatic_gvcfs": {
        "mem": "96g",
        "threads": "1",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_1": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_10": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_11": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_12": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_13": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_14": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_15": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_16": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_17": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_18": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_19": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_2": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_20": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_21": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_22": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_3": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_4": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_5": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_6": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_7": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_8": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_9": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_MT": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_X": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_gvcfs_Y": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_genotype_somatic_gvcfs": {
        "mem": "96g",
        "threads": "4",
        "time": "10-00:00:00"
    },
    "gatk_genotyping": {
        "threads": "1",
        "time": "4-00:00:00"
    },
    "gatk_haplotype_caller": {
        "mem": "64g",
        "threads": "4",
        "time": "10-00:00:00"
    },
    "gatk_mutect2": {
        "mem": "48g",
        "threads": "4",
        "time": "10-00:00:00"
    },
    "gatk_realign": {
        "gres": "lscratch:500",
        "mem": "64g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "gatk_recal": {
        "mem": "64g",
        "threads": "16",
        "time": "5-00:00:00"
    },
    "gatk_rnaseqvar_haplotype_caller": {
        "mem": "96g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "gatk_select_variants_rnaseqvar": {
        "mem": "64g",
        "threads": "1",
        "time": "3-00:00:00"
    },
    "gatk_splitcigar": {
        "mem": "96g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "gatk_variant_annnotator": {
        "mem": "64g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "gatk_variant_recal": {
        "mem": "64g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "GEM": {
        "mem": "32g",
        "threads": "32"
    },
    "germline_filter_rnaseqvar": {
        "mem": "64g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "HOMER_motif": {
        "threads": "48"
    },
    "integratedBatch":{
        "threads": "8",
        "mem": "200g",
        "time": "2-00:00:00"
    },
    "kraken_pe": {
        "cpus-per-task": "24",
        "gres": "lscratch:256",
        "mem": "110g"
    },
    "kraken_se": {
        "cpus-per-task": "24",
        "gres": "lscratch:256",
        "mem": "110g"
    },
    "make_germline_network": {
        "mem": "64g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "make_somatic_network": {
        "mem": "64g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "manta_germline": {
        "mem": "96g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "manta_somatic": {
        "mem": "96g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "manta_wgs": {
        "mem": "96g",
        "threads": "8",
        "time": "10-00:00:00"
    },
    "MEMEChIP": {
        "mem": "64g",
        "threads": "32"
    },
    "mirdeep2": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "mirdeep2_1p": {
        "mem": "16g",
        "threads": "4",
        "time": "1-00:00:00"
    },
    "mirdeep2_2p": {
        "mem": "16g",
        "threads": "16",
        "time": "1-00:00:00"
    },
    "mirdeep2_mapper": {
        "mem": "16g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "mirdeep2_single":{
        "mem": "16g",
        "threads": "16",
        "time": "1-00:00:00"
    },
    "mirseq_gencode_classification": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "mirseq_init": {
        "mem": "16g",
        "threads": "1",
        "time": "5-00:00:00"
    },
    "mirseq_main_document": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "mirseq_make_bams": {
        "mem": "32g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "mirseq_make_bams_bwa": {
        "mem": "32g",
        "threads": "1",
        "time": "4-00:00:00"
    },
    "mirseq_miRspring_bowtie": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "mirseq_miRspring_bwa": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "mirseq_summarize": {
        "mem": "16g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "mirseq_targetscan": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "mirseq_variants": {
        "mem": "16g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "multiqc": {
        "mem": "24g",
        "threads": "2",
        "time": "1-00:00:00"
    },
    "ngsplot": {
        "mem": "48g"
    },
    "ngsqc": {
        "threads": "1",
        "mem":"120g"
    },
    "novo_sort": {
        "mem": "120g",
        "threads": "8",
        "time": "2-00:00:00"
    },
    "novocraft_novoalign": {
        "threads": "32",
        "time": "6-00:00:00"
    },
    "novocraft_sort": {
        "mem": "120g",
        "threads": "8",
        "gres": "lscratch:500",
        "time": "2-00:00:00"
    },
    "oncofuse": {
        "mem": "48g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "pca": {
        "mem": "88g",
        "threads": "2",
    },
    "picard": {
        "gres": "lscratch:256",
        "mem": "110g",
        "threads": "6"
    },
    "picard_dedup": {
        "gres": "lscratch:256",
        "mem": "96g",
        "threads": "2"
    },
    "picard_headers": {
        "threads": "1",
        "time": "2-00:00:00"
    },
    "picard_headers2": {
        "mem": "24g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "picard_index_bam": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "picard_markdups": {
        "threads": "12",
        "time": "2-00:00:00"
    },
    "picard_rnaseqvar_markdups": {
        "threads": "1",
        "time": "2-00:00:00"
    },
    "picard_rnaseqvarheaders": {
        "threads": "1",
        "time": "2-00:00:00"
    },
    "pindel_germline": {
        "mem": "64g",
        "threads": "8"
    },
    "ppqt": {
        "mem": "24g"
    },
    "preseq": {
        "mem": "24g"
    },
    "qc_scrna":{
        "threads": "1",
        "mem": "150g",
        "time": "1-00:00:00"
    },
    "qcReport_scrna":{
        "threads": "1",
        "mem": "48g",
        "time": "1:00:00"
    },
    "qualibam": {
        "threads": "8",
        "mem": "12g",
        "time": "1-00:00:00"
        },
    "qualimap": {
        "mem": "96g",
        "threads": "8",
        "time": "4-00:00:00"
    },
    "qualimap_rna": {
        "mem": "96g",
        "threads": "8",
        "time": "4-00:00:00"
    },
    "qualimap_wgs": {
        "mem": "96g",
        "threads": "8",
        "time": "4-00:00:00"
    },
    "rawfastqc": {
        "threads": "8"
    },
    "rnafusioncleanup": {
        "mem": "12g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "rsem": {
        "gres": "lscratch:500",
        "threads": "16",
        "time": "4-00:00:00"
    },
    "salmon": {
        "mem": "110g",
        "threads": "6",
        "time": "1-00:00:00"
    },
    "samtools_flagstats": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "samtools_flagstats_dedup": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "samtools_mpileup": {
        "threads": "1",
        "time": "5-00:00:00"
    },
    "samtools_sam2bam": {
        "threads": "1",
        "time": "2-00:00:00"
    },
    "samtools_sort": {
        "threads": "1",
        "time": "2-00:00:00"
    },
    "script_batchgvcf": {
        "mem": "12g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "script_bzip2": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "script_checkqc": {
        "threads": "1",
        "time": "4-00:00:00"
    },
    "script_coverage_qc": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "script_somatic_batchgvcf": {
        "mem": "12g",
        "threads": "1",
        "time": "1-00:00:00"
    },
    "script_split_gvcfs": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "scrna_cca": {
        "mem": "100g",
        "threads": "4"
    },
    "scrna_cluster": {
        "mem": "100g",
        "threads": "4"
    },
    "scrna_initial": {
        "mem": "100g",
        "threads": "4"
    },
    "scrna_jackstraw": {
        "mem": "100g",
        "threads": "4"
    },
    "scrna_multicluster": {
        "mem": "100g",
        "threads": "4"
    },
    "sleuth": {
        "mem": "110g",
        "threads": "4"
    },
    "snpeff": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "snpeff_dbnsfp": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "somatic_germline_calls": {
        "mem": "64g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "star1p": {
        "mem": "110g",
        "threads": "32",
        "time": "4-00:00:00"
    },
    "star2p": {
        "mem": "110g",
        "threads": "32",
        "time": "4-00:00:00"
    },
    "star_align_1": {
        "mem": "96g",
        "threads": "32",
        "time": "4-00:00:00"
    },
    "star_align_2": {
        "mem": "96g",
        "threads": "32",
        "time": "5-00:00:00"
    },
    "star_generate": {
        "threads": "1",
        "time": "1-00:00:00"
    },
    "starfusion": {
        "mem": "48g",
        "threads": "16",
        "time": "3-00:00:00"
    },
    "fusioninspector": {
        "mem": "48g",
        "threads": "16",
        "time": "3-00:00:00"
    },
    "fusioninsp": {
        "mem": "64g",
        "threads": "16",
        "time": "3-00:00:00"
    },
    "fusioninsp_fuscatch": {
        "mem": "64g",
        "threads": "16",
        "time": "3-00:00:00"
    },
    "fusioninsp_starfus": {
        "mem": "96g",
        "threads": "16",
        "time": "3-00:00:00"
    },
    "stats": {
        "gres": "lscratch:256",
        "mem": "110g",
        "threads": "4"
    },
    "strelka": {
        "mem": "64g",
        "threads": "4",
        "time": "5-00:00:00"
    },
    "subread": {
        "gres": "lscratch:500",
        "threads": "16",
        "time": "1-00:00:00"
    },
    "subreadoverlap": {
        "gres": "lscratch:500",
        "threads": "16",
        "time": "1-00:00:00"
    },
    "svaba_germline": {
        "mem": "96g",
        "threads": "32",
        "time": "10-00:00:00"
    },
    "theta": {
        "mem": "48g",
        "threads": "1",
        "time": "2-00:00:00"
    },
    "trim": {
        "mem": "66g",
        "threads": "16",
        "time": "5-00:00:00"
    },
    "trim_pe": {
        "mem": "120g",
        "threads": "32"
    },
    "trim_se": {
        "mem": "120g",
        "threads": "32"
    },
    "trim_step4": {
        "threads": "16"
    },
    "trimmomatic": {
        "mem": "24g",
        "threads": "32",
        "time": "5-00:00:00"
    },
    "trimmomatic_pe": {
        "mem": "24g",
        "threads": "32",
        "time": "4-00:00:00"
    },
    "varscan": {
        "threads": "1",
        "time": "4-00:00:00"
    },
    "vcf2maf_mutect": {
        "mem": "96g",
        "threads": "2",
        "time": "1-00:00:00"
    },
    "vcf2maf_mutect2": {
        "mem": "96g",
        "threads": "2",
        "time": "1-00:00:00"
    },
    "vcf2maf_strelka": {
        "mem": "96g",
        "threads": "2",
        "time": "1-00:00:00"
    },
    "vcf2maf_tumoronly": {
        "mem": "96g",
        "threads": "2",
        "time": "1-00:00:00"
    },
    "wgs_theta": {
        "mem": "48g",
        "threads": "1",
        "time": "2-00:00:00"
    }
}