database_creation.json

{
    "sample": "testproject02",
    "ressources": {
        "threads": 28,
        "megahit_memory": 0.9,
        "metaspades_memory": 230
    },
    "preprocessing": {
        "run_trimmomatic": {
            "mode": "PE",
            "illuminaclip": "/data/miniconda3/envs/mpies/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10",
            "leading": 3,
            "trailing": 3,
            "slidingwindow": "4:15",
            "minlen": 36
        }
    },
    "assembled": {
        "run_assembly": true,
        "assembler": "megahit",
        "run_megahit": {
            "klist": "21,33,55,77,99,127"
        },
        "run_genecalling": true,
        "prodigal": {
            "mode": "meta"
        }
    },
    "unassembled": {
        "run_fraggenescan": {
            "train_file": "illumina_1"
        }
    },
    "otu_table": {
        "run_singlem": false,
        "generate_otu_table": {
            "mode": "pipe"
        },
        "obtain_tax_list": {
            "mode": "parse_singlem",
            "cutoff": 1
        },
        "obtain_proteome": {
            "mode": "amplicon"
        }
    },
    "functional_subset": {
        "toml_file": "functional_subset.toml",
        "mode": "function_subset"
    },
    "postprocessing": {
        "remove_short_sequences": {
            "min_length": 30
        },
        "hash_headers": {
            "mode": "hashing",
            "hash_type": "md5"
        }
    }
}