DATA:
    FASTQ: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/fastq/
    FAST5: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/fast5/
    ILLUMINA: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/illumina/
    GENOME_SIZE: 4.8m
    REF: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/ref/BAI3_Sanger.fsa
    OUTPUT: /home/comte/Documents/IPME/CulebrONT_pipeline/CulebrONT_OUTPUT/
ASSEMBLY:
    CANU: true
    FLYE: true
    MINIASM: true
    RAVEN: true
    SMARTDENOVO: true
    SHASTA: true
POLISHING:
    RACON: true
CIRCULAR: true
CORRECTION:
    NANOPOLISH: true
    MEDAKA: true
    PILON: true
FIXSTART: true
QUALITY:
    BUSCO: true
    QUAST: true
    BLOBTOOLS: true
    ASSEMBLYTICS: true
    FLAGSTATS: true
    KAT: true
MSA:
    MAUVE: true
params:
    MINIMAP2:
        PRESET_OPTION: map-ont
    FLYE:
        OPTIONS: ''
    CANU:
        OPTIONS: gridOptions="-p long" useGrid=true
    SMARTDENOVO:
        KMER_SIZE: 16
        OPTIONS: -J 5000
    SHASTA:
        MEM_MODE: filesystem
        MEM_BACKING: disk
        OPTIONS: --Reads.minReadLength 0
    CIRCLATOR:
        OPTIONS: ''
    RACON:
        RACON_ROUNDS: 2
    CORRECTION_MAKERANGE:
        SEGMENT_LEN: '50000'
        OVERLAP_LEN: '200'
    NANOPOLISH:
        OPTIONS: ''
    MEDAKA:
        MEDAKA_TRAIN_WITH_REF: false
        MEDAKA_MODEL_PATH: r941_min_high_g303
        MEDAKA_FEATURES_OPTIONS: --batch_size 10 --chunk_len 100 --chunk_ovlp 10
        MEDAKA_TRAIN_OPTIONS: '--batch_size 10 --epochs 500 '
        MEDAKA_CONSENSUS_OPTIONS: '--batch 200 '
    PILON:
        PILON_ROUNDS: 2
        OPTIONS: ''
    BUSCO:
        DATABASE: 'bacteria_odb10 --update-data '
        MODEL: genome
        SP: ''
    QUAST:
        GFF: ''
        OPTIONS: --large
        GENOME_SIZE_PB: 4800000
    DIAMOND:
        DATABASE: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/testBacteria.dmnd
    MUMMER:
        MINMATCH: 100
        MINCLUSTER: 500
    ASSEMBLYTICS:
        UNIQUE_ANCHOR_LEN: 10000
        MIN_VARIANT_SIZE: 50
        MAX_VARIANT_SIZE: 10000
    BLOBTOOLS:
        NAMES: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/blobtools/names.dmp
        NODES: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/blobtools/nodes.dmp