annotation.json

{
    "sample": "virusDB",
    "excel_file_no_ext": "2J2SET13 2JSET11 2N2SET14 2NSET12",
    "ressources": {
        "threads": 28
    },
    "subset_sequences": {
        "mode": "subset_sequences"
    },
    "taxonomy": {
        "protein_groups": {
            "mode": "protein_groups"
        },
        "run_taxonomy": true,
        "run_diamond": {
            "mode": "blastp",
            "output_format": 6,
            "diamond_database": "/data/mpies/taxonomy/nr.20190408.dmnd",
            "max_target_seqs": 20,
            "score": 80,
            "compress": 0,
            "sensitive": ""
        },
        "run_blast2lca": {
            "binary": "/data/megan/tools/blast2lca",
            "input_format": "BlastTab",
            "blast_mode": "BlastP",
            "acc2tax_file": "/data/megan/data/prot_acc2tax-Nov2018X1.abin"
        },
        "parse_taxonomy": {
            "mode": "taxonomy"
        }
    },
    "functions": {
        "protein_groups": {
            "mode": "protein_groups"
        },
        "run_functions_cog": true,
        "run_cog": {
            "run_diamond": {
                "mode": "blastp",
                "output_format": 6,
                "diamond_database": "/data/mpies/functions/cog/cog.dmnd",
                "max_target_seqs": 20,
                "score": 80,
                "compress": 0,
                "sensitive": ""
            },
            "parse_functions_cog": {
                "mode": "functions_cog"
            },
            "cog_table": "/data/mpies/functions/cog/cog2003-2014.csv",
            "cog_names": "/data/mpies/functions/cog/cognames2003-2014.tab",
            "cog_functions": "/data/mpies/functions/cog/fun2003-2014.tab"
        },
        "run_functions_uniprot": true,
        "run_uniprot": {
            "run_diamond": {
                "mode": "blastp",
                "output_format": 6,
                "diamond_database": "/data/mpies/functions/uniprot/uniprot_trembl.20190709.dmnd",
                "max_target_seqs": 20,
                "score": 80,
                "compress": 0,
                "sensitive": "--sensitive"
            },
            "parse_functions_uniprot": {
                "mode": "functions_uniprot",
                "go_annotation": ""
            },
            "uniprot_table": "/data/mpies/functions/uniprot/uniprot_trembl.20190709.table.gz"
        }
    },
    "export_tables": {
        "mode": "export_tables"
    }
}