auto-pangolin

Automated lineage calling of SARS-CoV-2 sequence data using the BCCDC-PHL/pangolin-nf pipeline.

Installation

Usage

Start the tool as follows:

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

Configuration

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

{
    "analysis_parent_dir": "/path/to/analysis_by_run",
    "analysis_work_dir": "/path/to/work-auto-pangolin",
    "analysis_output_dir": "/path/to/pangolin_lineages_by_date",
    "notification_email_addresses": [
	"[email protected]"
    ],
    "send_notification_emails": false,
    "analysis_time": "07:00",
    "pipelines": [
	{
	    "pipeline_name": "BCCDC-PHL/pangolin-nf",
	    "pipeline_version": "v0.4.0",
	    "pipeline_parameters": {
		"analysis_parent_dir": null,
		"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"}}