/routine-nanopore-qc-collector

Collect Routine QC for Nanopore Sequence Data

Primary LanguagePython

Routine Nanopore QC Collector

Collects QC metrics from the BCCDC-PHL/routine-nanopore-qc pipeline. Outputs are supplied to the BCCDC-PHL Routine Nanopore QC site

Usage

usage: routine-nanopore-qc-collector [-h] [-c CONFIG] [--log-level LOG_LEVEL]

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
  --log-level LOG_LEVEL

routine-nanopore-qc-collector -c config.json

Configuration

The tool takes a single config file, in json format. A config_template.json is provided in this repo:

{
    "analysis_by_run_dir": "/path/to/analysis_by_run",
    "excluded_runs_list": "/path/to/excluded_runs.csv",
    "known_species_list": "/path/to/known_species.csv",
    "scan_interval_seconds": 3600,
    "output_dir": "/path/to/routine-nanopore-qc-collector/data"
}