config.imp.json

{
    "General": {
      "threads": 4,
      "memory_total_gb": 8,
      "memory_per_core_gb": 2,
      "tmp_dir": "./build/tmp",
      "imp_src": "src",
      "datadir": "TEST_DATA",
      "raws": {
          "Metagenomics": "MG.R1.5_percent.fq MG.R2.5_percent.fq",
          "Metatranscriptomics": "MT.R1.5_percent.fq MT.R2.5_percent.fq"
      },
      "sample": "test",
      "outputdir": "build",
      "db_path": "db"
    },
    "Preprocessing": {
      "filtering": true,
      "trimmomatic": {
          "adapter": "TruSeq3",
          "leading": 20,
          "minlen": 40,
          "palindrome_clip_threshold": 30,
          "simple_clip_threshold": 10,
          "trailing": 20,
          "seed_mismatch": 2,
          "window_size": 1,
          "window_quality": 3,
          "strictness": 0.5,
          "target_length": 40,
          "jarfile": "/home/imp/lib/trimmomatic-0.32.jar"
      }
    },
    "Assembly": {
      "idba_ud": {
          "mink": 25,
          "maxk": 95,
          "step": 5,
          "perid": 0.98
      }
    },
    "Analysis": {
      "vizbin": {
          "dimension": 50,
          "length": 5,
          "size": 4,
          "theta": 0.5,
          "perp": 1,
          "minlen": 1000
      }
    },
    "Util": {
    },
    "human_filtering": {
        "filter": "chr21",
        "url": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr21.fa.gz"
    },
    "sortmerna": {
        "pkg_url": "https://github.com/biocore/sortmerna/archive/2.0.tar.gz",
        "scripts_path": "/home/imp/lib",

        "files": [
            "rfam-5.8s-database-id98",
            "silva-arc-16s-id95",
            "silva-bac-16s-id90",
            "silva-euk-18s-id95",
            "rfam-5s-database-id98",
            "silva-arc-23s-id98",
            "silva-bac-23s-id98",
            "silva-euk-28s-id98"
        ]
    },
    "prokka": {
        "pkg_url": "http://www.vicbioinformatics.com/prokka-1.11.tar.gz",
        "databases": [
            "cm/Bacteria.i1i",
            "genus/Staphylococcus.phr",
            "hmm/CLUSTERS.hmm.h3f",
            "kingdom/Archaea/sprot.phr"
        ]
    }
}