{
    "samples_txt": "samples.txt",
    "remove_short_reads_based_on_references": {
        "delimiter-for-iu-remove-ids-from-fastq": " ",
        "dont_remove_just_map": true,
        "references_for_removal_txt": "mock_ref_for_removal.txt"
    },
    "idba_ud": {
        "--min_contig": 1000,
        "threads": 11,
        "run": true,
        "--mink": "",
        "--maxk": "",
        "--step": "",
        "--inner_mink": "",
        "--inner_step": "",
        "--prefix": "",
        "--min_count": "",
        "--min_support": "",
        "--seed_kmer": "",
        "--similar": "",
        "--max_mismatch": "",
        "--min_pairs": "",
        "--no_bubble": "",
        "--no_local": "",
        "--no_coverage": "",
        "--no_correct": "",
        "--pre_correction": ""
    },
    "iu_filter_quality_minoche": {
        "run": false
    },
    "output_dirs": {
        "FASTA_DIR": "02_FASTA_idba_ud_no_qc",
        "CONTIGS_DIR": "03_CONTIGS_idba_ud_no_qc",
        "QC_DIR": "01_QC_idba_ud_no_qc",
        "MAPPING_DIR": "04_MAPPING_idba_ud_no_qc",
        "PROFILE_DIR": "05_ANVIO_PROFILE_idba_ud_no_qc",
        "MERGE_DIR": "06_MERGED_idba_ud_no_qc",
        "SHORT_READ_FILTER_DIR": "01_SHORT_READ_FILTER_idba_ud_no_qc",
        "LOGS_DIR": "00_LOGS_idba_ud_no_qc"
    }
}
