auto-flu

Automated analysis of flu sequence data using the BCCDC-PHL/fluviewer-nf pipeline.

Installation

Usage

Start the tool as follows:

auto-flu --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-flu --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-flu-work",
  "excluded_runs_list": "/path/to/excluded_runs.csv",
  "notification_email_addresses": [
	"someone@example.org",
	"someone_else@example.org"
  ],
  "send_notification_emails": true,
  "scan_interval_seconds": 3600,
  "pipelines": [
    {
      "pipeline_name": "BCCDC-PHL/fluviewer-nf",
      "pipeline_version": "v0.3.0",
      "pipeline_parameters": {
  	    "fastq_input": null,
   	    "db": "/path/to/FluViewer_db.fa",
   	    "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"}}