{
    "out_dir": "/home/usuario/epi2melabs/instances/wf-hereditary-cancer_01M2GGC8ZRPEP156W9D3WKNMV7/output",
    "wf": {
        "e2l_base_tag": "sha8ecee6d351b0c2609b452f3a368c390587f6662d",
        "e2l_snp_tag": "sha8cc7e88ff71bf593d7852309a31d3adb29a7caeb",
        "e2l_sv_tag": "sha8134f9fef5e19605c7fb4c1348961d6771f1af79",
        "e2l_mod_tag": "shaa7bf2b62946eeb7646b9b9d60b892edfc3b3a52c",
        "cnv_tag": "sha428cb19e51370020ccf29ec2af4eead44c6a17c2",
        "str_tag": "shadd2f2963fe39351d4e0d6fa3ca54e1064c6ec057",
        "spectre_tag": "sha42472d37a5a992c3ee27894a23dce5e2fff66d27",
        "snpeff_tag": "shaff5aecfe85e945f49215fa3d43b9ed4ae352bd5c",
        "common_sha": "sha72f3517dd994984e0e2da0b97cb3f23f8540be4b",
        "longphase_tag": "sha4ff1cd9a6eee338a414082cb24f943bcc4ce8e7c",
        "agent": "epi2melabs/5.4.0",
        "epi2me_user": "guest",
        "epi2me_instance": "01M2GGC8ZRPEP156W9D3WKNMV7",
        "name": "wf-hereditary-cancer",
        "example_cmd": [
            "--bam 'wf-hereditary-cancer-demo/chr5.reads.bam'"
        ]
    },
    "sv": true,
    "snp": true,
    "str": false,
    "mod": true,
    "bam_min_coverage": 10,
    "depth_window_size": 25000,
    "annotation": false,
    "phased": true,
    "include_all_ctgs": false,
    "output_report": true,
    "haplocheck": false,
    "igv": true,
    "cluster_merge_pos": 150,
    "min_sv_length": 30,
    "sv_benchmark": false,
    "ref_pct_full": 0.1,
    "var_pct_full": 0.7,
    "snp_min_af": 0.08,
    "indel_min_af": 0.15,
    "min_cov": 2,
    "min_mq": 5,
    "min_qual": 2,
    "min_contig_size": 0,
    "refine_snp_with_sv": true,
    "force_strand": false,
    "depth_intervals": false,
    "GVCF": false,
    "base_err": 0.001,
    "gq_bin_size": 5,
    "downsample_coverage": false,
    "downsample_coverage_target": 60,
    "downsample_coverage_margin": 1.1,
    "output_xam_fmt": "bam",
    "alignment_report_coverage_threshold": 30,
    "threads": 4,
    "ubam_map_threads": 8,
    "ubam_sort_threads": 3,
    "ubam_bam2fq_threads": 1,
    "modkit_threads": 4,
    "disable_ping": false,
    "help": false,
    "version": false,
    "sample_name": "OMICS_14",
    "bam": "/var/lib/minknow/data/20260902/HCP_sample_4_5_6/20260902_1532_P2S-03417-B_PBM52225_4f92217b/bam_pass/barcode05",
    "store_dir": "/home/usuario/epi2melabs/data",
    "aws_image_prefix": null,
    "aws_queue": null,
    "sv_benchmark_vcf": null,
    "sv_benchmark_bed": null,
    "coverage_bed": "/home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-coverage-bed/1/HCP_Exon.bed",
    "ref": "/home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-ref/1/HCP_hg38_alt.masked.fasta",
    "bed": "/home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-bed/1/HCP_Gene.bed",
    "sex": null,
    "mitogenome": null,
    "override_basecaller_cfg": null,
    "clair3_model_path": null,
    "ctg_name": null,
    "vcf_fn": null,
    "tr_bed": null,
    "min_read_support": "auto",
    "min_read_support_limit": 2,
    "sniffles_args": null,
    "modkit_args": null,
    "partner": null,
    "monochrome_logs": false,
    "validate_params": true,
    "show_hidden_params": false,
    "schema_ignore_params": "show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,min_read_support,min_read_support_limit,fastq_only"
}