{
  "config": {
    "DEFAULT": {
      "bam_dir": "./mapping/@BARCODE",
      "base": ".",
      "bcf_dir": "./calls/@BARCODE",
      "benchmark_mode": "true",
      "extra_references": "reference/conversion_control.fa.gz",
      "extract_dir": "./extract/@BARCODE",
      "gembs_dbfile": "file:gemBS?mode=memory&cache=shared",
      "index_dir": "indexes",
      "jobs": "3",
      "nonbs_flag": false,
      "reference": "reference/sacCer3.fa.gz",
      "report_dir": "./report",
      "sequence_dir": "./fastq/@SAMPLE",
      "threads": "8"
    },
    "calling": {
      "contig_pool_limit": "25000000",
      "conversion": [
        "0.01",
        "0.05"
      ],
      "haploid": "False",
      "keep_duplicates": "False",
      "keep_improper_pairs": "False",
      "left_trim": "5",
      "mapq_threshold": "10",
      "omit_contigs": [
        "NC_001416.1",
        "NC_001604.1"
      ],
      "qual_threshold": "13",
      "reference_bias": "2",
      "remove_individual_bcfs": "True",
      "right_trim": "0"
    },
    "extract": {
      "bigwig_strand_specific": "True",
      "make_bedmethyl": "True",
      "make_bigwig": "True",
      "make_cpg": "True",
      "make_non_cpg": "True",
      "phred_threshold": "10",
      "strand_specific": "True"
    },
    "index": {
      "sampling_rate": "4"
    },
    "mapping": {
      "non_stranded": "False",
      "remove_individual_bams": "True",
      "underconversion_sequence": "NC_001416.1"
    },
    "report": {}
  },
  "contigs": {
    "@pool_1": [
      "chrIV",
      "chrXV",
      "chrVII",
      "chrXII",
      "chrXVI",
      "chrXIII",
      "chrII",
      "chrXIV",
      "chrX",
      "chrXI",
      "chrV",
      "chrVIII",
      "chrIX",
      "chrIII",
      "chrVI",
      "chrI",
      "chrM"
    ]
  },
  "sampleData": {
    "sample5": {
      "file": {
        "1": "sample5_data_1_200000.fastq.gz",
        "2": "sample5_data_2_200000.fastq.gz"
      },
      "sample_barcode": "sample_sample5",
      "sample_name": "sample5",
      "type": "PAIRED"
    }
  }
}