config.json

{
    "bowtie2_rules": {
        "platform": "Illumina",
        "mapping_params": {
            "default": ""
        },
        "load_env": "module load bioinfo-tools bowtie2/2.2.3 samtools/1.1"
    },
    "samtools_rules": {
        "load_env": "module load bioinfo-tools samtools/1.1 BEDTools/2.21.0 picard/1.118",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou"
    },
    "mapping_report_rules": {},
    "concoct_rules": {
        "load_env": "source activate concoct && module load bioinfo-tools MUMmer/3.23 # CONCOCT dev f4cb9fcb",
        "mapper": "bowtie2",
        "mapping_params": "default",
        "concoct_params": {
            "cutoff-1000-maxcluster-1000": "-c 1000 -l 1000"
        },
        "scripts_dir": "/home/alneberg/repos/CONCOCT/scripts"
    },
    "prodigal_rules": {
        "load_env": "module load bioinfo-tools prodigal/2.60",
        "prodigal_params": {
            "default-meta": "-p meta"
        }
    },
    "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",
        "EXTEND": {
            "gff": "toolbox/scripts/extended_prokka/extend_gff.py"
        },
        "get_prokka_annotation_script": "toolbox/scripts/extended_prokka/get.prokka.annotation.sh",
        "collate_annotations_script": "toolbox/scripts/extended_prokka/collate.annotations.py",
        "prokka_ops": "--metagenome",
        "contigs": {},
        "threads": "2"
    },
    "rpsblast_rules": {
        "load_env": "module load bioinfo-tools blast/2.2.29+ 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"
    },
    "hmmer_rules": {
            "load_env": "module load bioinfo-tools hmmer/3.1b1-gcc",
            "hmmer_params": {
                "default-concoct": "-E 0.0001 --cpu 16"
            },
            "databases": {
                "all_pog": ""
            }
        },
    "assembly_dir": ["data/contigs"],
    "fastq_dirs": ["data/reads"],
    "toolbox_dir": "toolbox"
}