nf_build.json

{
    "aligner": {
        "mafft": {
            "name": "mafft",
            "op": 1.53,
            "ep": 0.123,
            "maxiterate": 1000,
            "matrix": "",
            "blosum_coefficient": 62,
            "pam_coefficient": 80,
            "auto": false,
            "localpair": true,
            "globalpair": false,
            "genafpair": false,
            "retree": 2,
            "nofft": false,
            "parttree": false
        }
    },
    "trimmer": {
        "trimal": {
            "name": "trimal",
            "gt": null,
            "st": null,
            "ct": null,
            "w": null,
            "gappyout": false,
            "strictplus": false,
            "automated1": false
        }
    },
    "tree_builder": {
        "fasttree": {
            "name": "fasttree",
            "aa_model": "JTT",
            "nt_model": "JC",
            "gamma": false,
            "bootstrap": 1000,
            "pseudo": true,
            "spr": 4,
            "mlacc": 2,
            "slownni": true
        }
    }
}