config.json

{
    "prokka_extended_rules": {
        "dbs": ["cog", "pfam", "tigr"],
        "prokka_name": "prokka_mod",
        "load_env": "source activate concoct && module load bioinfo-tools BioPerl blast/2.2.28+ hmmer prodigal gnuparallel",
        "cddid_all": "/proj/b2010008/nobackup/database/cddid_all.tbl",
        "get_prokka_annotation_script": "toolbox/scripts/extended_prokka/get.prokka.annotation.sh",
        "collate_annotations_script": "toolbox/scripts/extended_prokka/collate.annotations.py",
        "prokka_ops": "-k Bacteria",
        "EXTEND": {
            "gff": "toolbox/scripts/extended_prokka/extend_gff.py"
        },
        "contigs": {},
        "threads": "4"
    },
    "rpsblast_rules": {
        "load_env": "module load bioinfo-tools blast/2.2.28+ gnuparallel/20140222",
        "rpsblast_params": {
            "default-concoct": "-outfmt '6 qseqid sseqid evalue pident score qstart qend sstart send length slen' -max_target_seqs 1 -evalue 0.00001"
        },
        "databases": {
            "cog": "/sw/data/uppnex/cdd/little_endian/Cog"
        },
        "parallel_params": "-N 10 --env PATH"
    },
    "toolbox_dir": "toolbox"
}