run_pheniqs.json

{
    "input": [
        "Undetermined_R1.fastq.gz",
        "Undetermined_R2.fastq.gz",
        "Undetermined_R3.fastq.gz",
        "Undetermined_R4.fastq.gz"
    ],
        "template": {
        "transform": { "token": [ "0::", "1::" , "3::" ] }
    },
    "multiplex": {
        "transform": { "token": [ "2::8" ] },
        "codec": {
            "@GTCAAGTT": { "barcode": [ "GTCAAGTT" ],
                           "output": [
                                        "ETX4_1_R1.fastq.gz",
                                        "ETX4_1_R2.fastq.gz",
                                        "ETX4_1_R3.fastq.gz",
                                        "ETX4_1_R4.fastq.gz"
          ]},
            "@GGCATAGG": { "barcode": [ "GGCATAGG" ],
                           "output": [
                                        "ETX4_2_R1.fastq.gz",
                                        "ETX4_2_R2.fastq.gz",
                                        "ETX4_2_R3.fastq.gz",
                                        "ETX4_2_R4.fastq.gz"
          ]},
            "@CTTGCAGA": { "barcode": [ "CTTGCAGA" ],
                           "output": [
                                        "ETX4_3_R1.fastq.gz",
                                        "ETX4_3_R2.fastq.gz",
                                        "ETX4_3_R3.fastq.gz",
                                        "ETX4_3_R4.fastq.gz"
          ]},
            "@CTATTCAA": { "barcode": [ "CTATTCAA" ],
                           "output": [
                                        "ETX4_G4_R1.fastq.gz",
                                        "ETX4_G4_R2.fastq.gz",
                                        "ETX4_G4_R3.fastq.gz",
                                        "ETX4_G4_R4.fastq.gz"
          ]},
             "@TGGTAACG": { "barcode": [ "TGGTAACG" ],
                           "output": [
                                        "NE55_1_R1.fastq.gz",
                                        "NE55_1_R2.fastq.gz",
                                        "NE55_1_R3.fastq.gz",
                                        "NE55_1_R4.fastq.gz"
          ]}
        },
        "algorithm": "pamld",
        "noise": 0.02,
        "confidence threshold": 0.95
    },
  "undetermined": {
      "output": [
          "undetermined_R1.fastq.gz",
          "undetermined_R2.fastq.gz",
          "undetermined_R3.fastq.gz",
          "undetermined_R4.fastq.gz"
      ]
  }
}