{
  "metric_profile": "ont_native",
  "output_dir": ".work",
  "default_reference": "dm6",
  "references": {
    "dm6": {
      "assembly": "dm6",
      "primary_chromosomes": [
        "chr2L",
        "chr2R",
        "chr3L",
        "chr3R",
        "chr4",
        "chrX"
      ],
      "fasta": "/path/to/dm6.fa",
      "chrom_sizes": "/path/to/dm6.chrom.sizes",
      "annotation": "/path/to/dm6.ncbiRefSeq.gtf",
      "bowtie2_index": "/path/to/dm6",
      "bwa_mem2_index": "/path/to/dm6.fa",
      "mycoplasma_index": "/path/to/index"
    },
    "hg38": {
      "assembly": "hg38",
      "primary_chromosomes": [
        "chr1",
        "chr2",
        "chr3",
        "chr4",
        "chr5",
        "chr6",
        "chr7",
        "chr8",
        "chr9",
        "chr10",
        "chr11",
        "chr12",
        "chr13",
        "chr14",
        "chr15",
        "chr16",
        "chr17",
        "chr18",
        "chr19",
        "chr20",
        "chr21",
        "chr22",
        "chrX"
      ],
      "fasta": "/path/to/hg38.fa",
      "chrom_sizes": "/path/to/hg38.chrom.sizes",
      "annotation": "/path/to/hg38.ncbiRefSeq.gtf",
      "bowtie2_index": "/path/to/hg38",
      "bwa_mem2_index": "/path/to/hg38.fa",
      "mycoplasma_index": "/path/to/index"
    }
  },
  "mycoplasma_screen": {
    "enabled": true,
    "target_contig_regex": "mycoplasma_target|mycoplasmopsis|mycoplasmoides|metamycoplasma|mesomycoplasma|acholeplasma|spiroplasma|ureaplasma|mollicutes",
    "minimum_screened_reads": 500
  },
  "spike_in": {
    "enabled": true,
    "mode": "auto",
    "database_manifest": "resources/spikein_v1/manifest.json",
    "declared_spike_in": false,
    "threads": 4,
    "minimum_aligned_bp": 80,
    "minimum_query_coverage": 0.8,
    "minimum_identity": 0.85
  },
  "alignment": {
    "chromatin_mapper": "bowtie2",
    "microc_mapper": "bwa-mem2"
  },
  "params": {
    "collision_qc_bin_size": 10000,
    "microc_minimum_contacts": 200,
    "microc_short_inward_bp": 200,
    "microc_minimum_query_coverage": 0.8,
    "microc_long_range_cis_min_bp": 10000,
    "minimum_raw_reads": 500,
    "minimum_complete_units": 200,
    "mapq": 20,
    "dedup_tolerance_bp": 0,
    "dedup_order": "after_contact_selection",
    "dedup_method": "exact unordered strand-aware aligned 5-prime endpoints within index scope",
    "metric_profile": "ont_native",
    "metric_definition_version": "2026.09.10",
    "ligation_minimum_segment_bp": 40,
    "ligation_minimum_query_coverage": 0.8,
    "ligation_maximum_query_gap": 30,
    "annotation_promoter_window_bp": 2000,
    "gene_profile_upstream_bp": 5000,
    "gene_profile_downstream_bp": 5000,
    "gene_profile_body_bp": 5000,
    "gene_profile_bin_size": 100,
    "gene_profile_sublibrary_threads": 16,
    "karyotype_bins_per_longest_chromosome": 250,
    "karyotype_gene_window_bp": 250000,
    "size_trace_max_bp": 2000,
    "size_trace_bandwidth": 0.045,
    "single_index_pair_fraction": 0.9,
    "index_variant_max_edit": 2,
    "index_variant_dominance_ratio": 5.0
  },
  "qc_reference_ranges": {
    "raw_reads": {
      "min": 500,
      "warning_min": 250
    },
    "mean_read_q": null,
    "complete_read_rate": {
      "min": 0.5,
      "max": 1.0,
      "warning_min": 0.3,
      "type": "percent"
    },
    "adapter_dimer_rate": {
      "min": 0.0,
      "max": 0.05,
      "warning_max": 0.1,
      "type": "percent"
    },
    "primary_mapping_rate": {
      "min": 0.5,
      "max": 1.0,
      "warning_min": 0.3,
      "type": "percent"
    },
    "usable_fragment_rate": {
      "min": 0.3,
      "max": 1.0,
      "warning_min": 0.15,
      "type": "percent"
    },
    "mitochondrial_fraction": {
      "min": 0.0,
      "max": 0.2,
      "warning_max": 0.4,
      "type": "percent"
    },
    "both_legs_mapping_rate": {
      "min": 0.5,
      "max": 1.0,
      "warning_min": 0.3,
      "type": "percent"
    },
    "cis_ratio": null
  },
  "samples": {
    "HL240": {
      "fastq": [
        "inputs/8KXMVK_4_CR_HL240.fastq"
      ],
      "type": "chromatin",
      "reference": "hg38"
    },
    "HL120": {
      "fastq": [
        "inputs/TVKRTF_11_MC_A_HL120.fastq"
      ],
      "type": "microc"
    }
  },
  "tools": {
    "python": "python3",
    "bowtie2": "bowtie2",
    "bwa_mem2": "bwa-mem2",
    "samtools": "samtools",
    "bamCoverage": "bamCoverage",
    "computeMatrix": "computeMatrix",
    "plotProfile": "plotProfile",
    "bedGraphToBigWig": "bedGraphToBigWig",
    "rscript": "Rscript"
  },
  "report_dir": "report"
}