config.sample.no-host-filtering.json

{
    "project" : "Trial_no-host-filtering",
    "tmpdir" : "/tmp",
    "adapters" : "/data/tools/Trimmomatic/0.36/adapters/NexteraPE-PE.fa",
    "min_qual" : "30",
    "min_length" : "150",
    "host_removal" : False,
    "reference" : "data/test-data/reference/beta-vulgaris-subset.fasta",
    "reference_index": "/data/genomes/Eukaryotes/Phaseolus_vulgaris/GCA_000499845.1_PhaVulg1_0_genomic",
    "emapper_database" : "/data/db/eggnogdb/5.0.0/",
    "emapper_diamond" : "/data/db/eggnogdb/5.0.0/eggnog_proteins.dmnd/",
    "CAT_database" : "/data/db/CAT/CAT_prepare_20200618/2020-06-18_CAT_database/",
    "CAT_taxonomy" : "/data/db/CAT/CAT_prepare_20200618/2020-06-18_taxonomy/",
    "CAT_database" : "/data/db/CAT/CAT_prepare_20200618/2020-06-18_CAT_database/",
    "CAT_taxonomy" : "/data/db/CAT/CAT_prepare_20200618/2020-06-18_taxonomy/",
    "filter_contigs_length" : "444",
    "filter_contigs_antismash" : "300",
    "assembler" : "megahit",
    "binner" : ["metabat", "vamb"],
    "big" : "bigscape",
    "kmers" : "33,55,77,99,127",
    "assembly-klist" : {
       "meta-large" : "27,37,47,57,67,77,87,97,107,117,127",
     },
    "treatment" : {
        "A" : ["B55"]
    },
    
    "data" : {
        "B55": { "forward":"data/B55_1.fq.gz", "rev":"data/B55_2.fq.gz"},
        "B57": { "forward":"data/B57_1.fq.gz", "rev":"data/B57_2.fq.gz"},
        "B83": { "forward":"data/B83_1.fq.gz", "rev":"data/B83_2.fq.gz"}
    }
}