Automated analysis of nanopore sequence data using the BCCDC-PHL/routine-nanopore-qc pipeline.
Start the tool as follows:
auto-routine-nanopore-qc --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-routine-nanopore-qc --config config.json --log-level debug
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-routine-nanopore-qc-work",
"notification_email_addresses": [
"someone@example.org",
"someone_else@example.org"
],
"send_notification_emails": true,
"scan_interval_seconds": 3600,
"pipelines": [
{
"pipeline_name": "BCCDC-PHL/routine-nanopore-qc",
"pipeline_version": "v0.1.0",
"pipeline_parameters": {
"fastq_input": null,
"kraken2_db": "/path/to/kraken2_db",
"outdir": null
}
}
]
}
This tool outputs structured logs in JSON Lines format:
Every log line should include the fields:
timestamplevelmodulefunction_nameline_nummessage
...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"}}