{
    "samples_txt": "samples.txt",
    "metaspades": {
        "additional_params": "--only-assembler",
        "threads": 11,
        "run": true,
        "use_scaffolds": ""
    },
    "remove_short_reads_based_on_references": {
        "delimiter-for-iu-remove-ids-from-fastq": " ",
        "references_for_removal_txt": "mock_ref_for_removal.txt"
    },
    "output_dirs": {
        "FASTA_DIR": "02_FASTA_metaspades",
        "CONTIGS_DIR": "03_CONTIGS_metaspades",
        "QC_DIR": "01_QC_metaspades",
        "MAPPING_DIR": "04_MAPPING_metaspades",
        "PROFILE_DIR": "05_ANVIO_PROFILE_metaspades",
        "MERGE_DIR": "06_MERGED_metaspades",
        "TAXONOMY_DIR": "07_TAXONOMY_metaspades",
        "LOGS_DIR": "00_LOGS_metaspades"
    }
}
