{
    "fasta_txt": "fasta.txt",
    "remove_short_reads_based_on_references": {
        "delimiter-for-iu-remove-ids-from-fastq": " ",
        "references_for_removal_txt": "mock_ref_for_removal.txt"
    },
    "references_mode": true,
    "collections_txt": "collections.txt",
    "anvi_summarize": {
        "run": true
    },
    "anvi_split": {
        "run": true
    },
    "output_dirs": {
        "FASTA_DIR": "02_FASTA_references_mode",
        "CONTIGS_DIR": "03_CONTIGS_references_mode",
        "QC_DIR": "01_QC_references_mode",
        "MAPPING_DIR": "04_MAPPING_references_mode",
        "PROFILE_DIR": "05_ANVIO_PROFILE_references_mode",
        "MERGE_DIR": "06_MERGED_references_mode",
        "LOGS_DIR": "00_LOGS_references_mode",
        "SHORT_READ_FILTER_DIR": "01_SHORT_READ_FILTER_references_mode"
    }
}
