auto-cpo

Automated analysis of carbapenemase-producing organism (CPO) sequence data.

Installation

Usage

Start the tool as follows:

auto-cpo --config config.json

See the Configuration section of this document for details on preparing a configuration file.

More detailed logs can be produced by controlling the log level using the --log-level flag:

auto-cpo --config config.json --log-level debug

Configuration

This tool takes a single config file, in JSON format, with the following structure:

{
    "fastq_by_run_dir": "/path/to/fastq_symlinks_by_run",
    "analysis_output_dir": "/path/to/analysis_by_run",
    "analysis_work_dir": "/path/to/auto-cpo-work",
    "conda_cache_dir": "/path/to/.conda/envs",
    "notification_email_addresses": [
    "someone@example.org"
    ],
    "send_notification_emails": false,
    "scan_interval_seconds": 3600,
    "analyze_runs_in_reverse_order": true,
    "qc_filters": {
    "samples": {
        "minimum_pre_alignment_estimated_depth_coverage_per_mb": 250,
        "warning_pre_alignment_estimated_depth_coverage_per_mb": 300,
        "minimum_q30_percent_before_filtering": 75,
        "warning_q30_percent_before_filtering": 80
    }
    },
    "pipelines_by_analysis_mode": {
    "short": [
        {
        "name": "BCCDC-PHL/basic-sequence-qc",
        "version": "v0.2.1",
        "dependencies": null,
        "parameters": {
            "fastq_input": null,
            "prefix": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/taxon-abundance",
        "version": "v0.1.7",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/basic-sequence-qc",
            "pipeline_version": "v0.2.1"
            }
        ],
        "parameters": {
            "samplesheet_input": null,
            "kraken_db": "/path/to/kraken2_db",
            "bracken_db": "/path/to/bracken_db",
            "read_length": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/routine-assembly",
        "version": "v0.4.5",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/basic-sequence-qc",
            "pipeline_version": "v0.2.1"
            }
        ],
        "parameters": {
            "samplesheet_input": null,
            "bakta": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/mlst-nf",
        "version": "v0.1.4",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/routine-assembly",
            "pipeline_version": "v0.4.5"
            }
        ],
        "parameters": {
            "assembly_input": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/plasmid-screen",
        "version": "v0.2.3",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/routine-assembly",
            "pipeline_version": "v0.4.5"
            }
        ],
        "parameters": {
            "samplesheet_input": null,
            "pre_assembled": null,
            "mob_db": "/path/to/mob-suite_db",
            "outdir": null
        }
        }
    ],
    "hybrid": [
        {
        "name": "BCCDC-PHL/basic-nanopore-qc",
        "version": "v0.1.0",
        "dependencies": null,
        "parameters": {
            "fastq_input": null,
            "prefix": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/plasmid-assembly",
        "version": "v0.1.1",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/basic-nanopore-qc",
            "pipeline_version": "v0.1.0"
            }
        ],
        "parameters": {
            "samplesheet_input": null,
            "hybrid": null,
            "chromosome_length": 250000,
            "db": "/path/to/plassembler_db",
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/mlst-nf",
        "version": "v0.1.4",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/plasmid-assembly",
            "pipeline_version": "v0.1.1"
            }
        ],
        "parameters": {
            "assembly_input": null,
            "outdir": null
        }
        },
        {
        "name": "BCCDC-PHL/plasmid-screen",
        "version": "v0.2.3",
        "dependencies": [
            {
            "pipeline_name": "BCCDC-PHL/plasmid-assembly",
            "pipeline_version": "v0.1.1"
            }
        ],
        "parameters": {
                    "samplesheet_input": null,
            "pre_assembled": null,
            "mob_db": "/path/to/mob-suite_db",
            "outdir": null
        }
        }
    ]
    }
}

Logging

This tool outputs structured logs in JSON Lines format:

Every log line should include the fields:

• timestamp
• level
• module
• function_name
• line_num
• message

...and the contents of the message key will be a JSON object that includes at event_type. The remaining keys inside the message will vary by event type.

{"timestamp": "2022-09-22T11:32:52.287", "level": "INFO", "module": "core", "function_name": "scan", "line_num": 56, "message": {"event_type": "scan_start"}}