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                            "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/excluded_loci.txt"
                        }
                    }
                ],
                "input_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK.vcf"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK_filtered.vcf"
                    }
                ]
            },
            {
                "step_number": 12,
                "name": "SnpEff",
                "description": "Annotates variants in VCF file",
                "version": "4.1",
                "prerequisite": [
                    {
                        "name": "M. tuberculosis H37Rv GenBank File",
                        "uri": {
                            "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/NC_000962.gbk"
                        }
                    }
                ],
                "input_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK_filtered.vcf"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK_annotated.vcf"
                    }
                ]
            },
            {
                "step_number": 13,
                "name": "parse_annotation.py",
                "description": "Parses annotated VCF to create annotation text file",
                "version": "",
                "input_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK_annotated.vcf"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_Final_annotation.txt"
                    }
                ]
            },
            {
                "step_number": 14,
                "name": "lineage_parser.py",
                "description": "Assigns Mycobacterium tuberculosis Complex lineage to isolate",
                "version": "",
                "prerequisite": [
                    {
                        "name": "Lineage Markers File",
                        "uri": {
                            "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/lineage_markers.txt"
                        }
                    }
                ],
                "input_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_Final_annotation.txt"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106.lineage_report.txt"
                    }
                ]
            },
            {
                "step_number": 15,
                "name": "BEDtools",
                "description": "Creates loci based coverage statistics of genome coverage",
                "version": "2.17.0",
                "input_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/bam_files/ERR552106.recalibrated.bam"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_genome_region_coverage.txt"
                    }
                ]
            },
            {
                "step_number": 16,
                "name": "resis_parser.py",
                "description": "Creates a coverage depth and width table of all loci in isolate genome",
                "version": "",
                "input_list": [
                    {
                        "uri": "[path_to_genome_loci_text_file]"
                    },
                    {
                        "uri": "[path_to_per_position_depth_text_file]"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_Coverage.txt"
                    }
                ]
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/CPTR-ReSeqTB/UVP/commit/9e8f588b3cd3f5eebde29f7d2879e1a1e1c1aed3"
                }
            }
        ],
        "script_driver": "Python",
        "software_prerequisites": [
            {
                "name": "BEDtools",
                "version": "2.17.0",
                "uri": {
                    "uri": "https://github.com/arq5x/bedtools/releases/tag/v2.17.0",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "5e4507c54355a4a38c6d3e7497a2836a123c6655"
                }
            },
            {
                "name": "Bcftools",
                "version": "1.2",
                "uri": {
                    "uri": "https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "352908143497da0640b928248165e83212dc4298"
                }
            },
            {
                "name": "BWA",
                "version": "0.7.12",
                "uri": {
                    "uri": "https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.12.tar.bz2/download",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "6389ca75328bae6d946bfdd58ff4beb0feebaedd"
                }
            },
            {
                "name": "FastQC",
                "version": "0.11.5",
                "uri": {
                    "uri": "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz",
                    "access_time": "2018-10-08T18:35:33-0400"
                }
            },
            {
                "name": "GATK",
                "version": "3.4.0",
                "uri": {
                    "uri": "https://github.com/broadgsa/gatk-protected/releases/tag/3.4",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "f19618653a0d23baaf147efe7f14aeb4eeb0cbb8"
                }
            },
            {
                "name": "Kraken",
                "version": "0.10.5",
                "uri": {
                    "uri": "https://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz",
                    "access_time": "2018-10-08T18:35:33-0400"
                }
            },
            {
                "name": "Picard",
                "version": "1.134",
                "uri": {
                    "uri": "https://github.com/broadinstitute/picard/releases/tag/1.134",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "a7a08c474e4d99346eec7a9956a8fe71943b5d80"
                }
            },
            {
                "name": "Pigz",
                "version": "2.3.3",
                "uri": {
                    "uri": "http://springdale.math.ias.edu/data/puias/unsupported/7/SRPMS/pigz-2.3.3-1.sdl7.src.rpm",
                    "access_time": "2018-10-08T18:35:33-0400"
                }
            },
            {
                "name": "Qualimap",
                "version": "2.11",
                "uri": {
                    "uri": "https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.1.1.zip",
                    "access_time": "2018-10-08T18:35:33-0400"
                }
            },
            {
                "name": "Samtools",
                "version": "1.2",
                "uri": {
                    "uri": "https://github.com/samtools/samtools/archive/1.2.zip",
                    "access_time": "2018-10-08T18:35:33-0400"
                }
            },
            {
                "name": "SnpEff",
                "version": "4.1",
                "uri": {
                    "uri": "https://sourceforge.net/projects/snpeff/files/snpEff_v4_1l_core.zip/download",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "c96e21564b05d6a7912e4dd35f9ef6fe2e094fbb"
                }
            },
            {
                "name": "Vcftools",
                "version": "0.1.12b",
                "uri": {
                    "uri": "https://sourceforge.net/projects/vcftools/files/vcftools_0.1.12.tar.gz/download",
                    "access_time": "2018-10-08T18:35:33-0400",
                    "sha1_checksum": "29a1ab67786e39be57cbb1ef4e0f6682110b7516"
                }
            }
        ],
        "external_data_endpoints": [
            {
                "name": "BCOReSeqTB",
                "url": "https://github.com/CPTR-ReSeqTB/UVP/"
            }
        ],
        "environment_variables": {
            "CORE": "8"
        }
    },
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "Mycobacterium tuberculosis H37Rv, complete genome",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/NC_000962.fa"
                }
            },
            {
                "uri": {
                    "filename": "Mycobacterium tuberculosis H37Rv, complete genome",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/NC_000962.gbk"
                }
            },
            {
                "uri": {
                    "filename": "excluded_loci",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/excluded_loci.txt"
                }
            },
            {
                "uri": {
                    "filename": "lineage_markers",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/lineage_markers.txt"
                }
            },
            {
                "uri": {
                    "filename": "variation sites",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_reference_files/snps.vcf"
                }
            },
            {
                "uri": {
                    "filename": "ERR552106_2.fastq.gz",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_input_fastq_files/ERR552106_2.fastq.gz"
                }
            },
            {
                "uri": {
                    "filename": "ERR552106_1.fastq.gz",
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_input_fastq_files/ERR552106_1.fastq.gz"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106.lineage_report.txt"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106.log"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_Coverage.txt"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106ERR552106_Final_annotation.txt"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK.vcf"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_GATK_filtered.vcf"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_Lineage.txt"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_deleted_loci.txt"
                }
            },
            {
                "mediatype": "text/csv",
                "uri": {
                    "uri": "http://bco.reseqtb.org/UVP-BCO/UVPv2.4.1_sample_results/ERR552106/ERR552106_genome_region_coverage.txt"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {
            "description": [
                "This test object represents tests done with single lineage sequences to establish the sensitivity of UVP to detect lineage and antibiotic resistant variants",
                "Test objective was to evaluate the ability of UVP to identify strain lineage and antibiotic resistant variants from samples of high, medium, low sequence qualities and depths of coverage of 10, 15, 20, 25 and 30-fold. Simulated reads developed from 12 lineage-specific M. tuberculosis (Mtb) genome sequences were used to test UVP."
            ],
            "parameters": {
                "sample_type": "single Mtb lineages (n = 12) with antibiotic resistant variants introduced in silico",
                "total_sample_size": "180",
                "platform": "Illumina HiSeq 2000",
                "paired_end": true,
                "length": "100",
                "simulated": true,
                "program": "ART",
                "simulator_parameters": [
                    {
                        "ss": "hs20"
                    },
                    {
                        "l": "100"
                    },
                    {
                        "m": "500"
                    },
                    {
                        "qU": "45"
                    },
                    {
                        "s": "100"
                    }
                ],
                "sequence_quality_level_parameters": {
                    "description": "these correspond to the ART parameters: qs, qs2, ir, ir2, dr, dr2.",
                    "sequence_quality_high": {
                        "substitution_error_rate_R1": "0.0004",
                        "substitution_error_rate_R2": "0.0007",
                        "insertion_error_rate_R1": "0.00009",
                        "insertion_error_rate_R2": "0.00015",
                        "deletion_error_rate_R1": "0.00011",
                        "deletion_error_rate_R2": "0.00023",
                        "units": "errors per sequenced base"
                    },
                    "sequence_quality_medium": {
                        "substitution_error_rate_R1": "0.004",
                        "substitution_error_rate_R2": "0.007",
                        "insertion_error_rate_R1": "0.0009",
                        "insertion_error_rate_R2": "0.0015",
                        "deletion_error_rate_R1": "0.0011",
                        "deletion_error_rate_R2": "0.0023",
                        "units": "errors per sequenced base"
                    },
                    "sequence_quality_low": {
                        "substitution_error_rate_R1": "0.04",
                        "substitution_error_rate_R2": "0.07",
                        "insertion_error_rate_R1": "0.009",
                        "insertion_error_rate_R2": "0.015",
                        "deletion_error_rate_R1": "0.011",
                        "deletion_error_rate_R2": "0.023",
                        "units": "errors per sequenced base"
                    }
                }
            },
            "summary results": {
                "sequence_quality_high": {
                    "sample size": "60",
                    "result": {
                        "lineage_assignment_rate": "93.33",
                        "mean_AR_identification_rate": "86.72",
                        "Units": "Percentage"
                    }
                },
                "sequence_quality_medium": {
                    "sample size": "60",
                    "result": {
                        "lineage_assignment_rate": "90.00",
                        "mean_AR_identification_rate": "81.00",
                        "Units": "Percentage"
                    }
                },
                "sequence_quality_low": {
                    "sample size": "60",
                    "result": {
                        "lineage_assignment_rate": "0.00",
                        "mean_AR_identification_rate": "0.00",
                        "Units": "Percentage"
                    }
                },
                "coverage_10": {
                    "sample size": "36",
                    "result": {
                        "lineage_assignment_rate": "41.67",
                        "mean_AR_identification_rate": "22.42",
                        "Units": "Percentage"
                    }
                },
                "coverage_15": {
                    "sample size": "36",
                    "result": {
                        "lineage_assignment_rate": "63.89",
                        "mean_AR_identification_rate": "57.14",
                        "Units": "Percentage"
                    }
                },
                "coverage_20": {
                    "sample size": "36",
                    "result": {
                        "lineage_assignment_rate": "66.67",
                        "mean_AR_identification_rate": "66.46",
                        "Units": "Percentage"
                    }
                },
                "coverage_25": {
                    "sample size": "36",
                    "result": {
                        "lineage_assignment_rate": "66.67",
                        "mean_AR_identification_rate": "66.66",
                        "Units": "Percentage"
                    }
                },
                "coverage_30": {
                    "sample size": "36",
                    "result": {
                        "lineage_assignment_rate": "66.67",
                        "mean_AR_identification_rate": "66.66",
                        "Units": "Percentage"
                    }
                }
            },
            "detailed results": [
                {
                    "sequence_quality_high": {
                        "coverage_10": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "66.67",
                                "mean_AR_identification_rate": "40.75",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_15": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "92.85",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_20": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "100.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_25": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "100.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_30": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "100.00",
                                "Units": "Percentage"
                            }
                        }
                    }
                },
                {
                    "sequence_quality_medium": {
                        "coverage_10": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "58.34",
                                "mean_AR_identification_rate": "26.50",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_15": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "91.66",
                                "mean_AR_identification_rate": "78.57",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_20": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "99.40",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_25": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "100.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_30": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "100.00",
                                "mean_AR_identification_rate": "100.00",
                                "Units": "Percentage"
                            }
                        }
                    }
                },
                {
                    "sequence_quality_low": {
                        "coverage_10": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "0.00",
                                "mean_AR_identification_rate": "0.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_15": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "0.00",
                                "mean_AR_identification_rate": "0.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_20": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "0.00",
                                "mean_AR_identification_rate": "0.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_25": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "0.00",
                                "mean_AR_identification_rate": "0.00",
                                "Units": "Percentage"
                            }
                        },
                        "coverage_30": {
                            "sample size": "12",
                            "result": {
                                "lineage_assignment_rate": "0.00",
                                "mean_AR_identification_rate": "0.00",
                                "Units": "Percentage"
                            }
                        }
                    }
                }
            ]
        },
        "algorithmic_error": {
            "placeholder": "for algorithmic error domain"
        }
    }
}
