auto-genoflu

An automated analysis workflow for running GenoFLU and managing outputs.

Usage

auto_genoflu -c <config_file> [--log-level {DEBUG,INFO,WARNING,ERROR}]

Arguments

• -c, --config: Path to JSON configuration file (required)
• --log-level: Set logging level (optional, default: INFO)

Operating Modes

Local Processing Mode (Default)

By default, the package operates in local processing mode:

auto_genoflu -c config.json

In this mode:

• Analysis is run locally on the machine
• No SLURM required

SLURM Processing Mode

To use SLURM for parallel processing, set "use_slurm": true in the config file:

auto_genoflu -c config.json

In this mode:

• Jobs are submitted to SLURM cluster
• Requires SLURM configuration in slurm_params

Nextcloud Integration

To use Nextcloud for file uploads, set "use_nextcloud": true in the config file:

In this mode:

• Files are uploaded via Nextcloud WebDAV API
• Directories are created via Nextcloud API
• Requires environment variables:
  • NEXTCLOUD_API_USERNAME
  • NEXTCLOUD_API_PASSWORD
  • NEXTCLOUD_API_URL

Configuration File

The configuration file should be a JSON file with the following structure:

{
    "id_threshold": 98.0,
    "input_dir": "/path/to/genoflu/inputs/",
    "output_dir": "/path/to/genoflu/outputs/",
    "provenance_dir": "/path/to/genoflu/logs/",
    "work_dir": "/path/to/working/dir",
    "summary_dir": "/path/to/genoflu/summary/",
    "glob_expressions": ["*.fa", "*.fasta", "*.fna"],
    "scan_interval_seconds": 180,
    "use_nextcloud": false,
    "use_slurm": false,
    "slurm_params": {
        "log_dir": "/path/to/slurm/logs",
        "partition": "prod",
        "cpus_per_task": 2,
        "mem": "4G",
        "time": "00:20:00",
        "job_name": "auto-genoflu_batch",
        "array_parallelism": 8
    }
}

Configuration Parameters

• id_threshold (optional): Identity threshold for GenoFLU analysis (default: 98.0)
• input_dir (required): Directory containing input FASTA files
• output_dir (required): Directory for output TSV files
• provenance_dir (required): Directory for provenance/log files
• work_dir (required): Directory where genoflu will execute and create temporary files
• summary_dir (required): Directory for summary files
• glob_expressions (optional): List of glob patterns for input files (default: [".fa", ".fasta", "*.fna"])
• scan_interval_seconds (optional): Time in seconds between scans for new files (default: 300)
• use_nextcloud (optional): Enable Nextcloud integration (default: false)
• use_slurm (optional): Enable SLURM processing (default: false)
• slurm_params (required if use_slurm is true): SLURM job parameters
  • log_dir: Directory for SLURM logs
  • partition: SLURM partition
  • cpus_per_task: CPUs per task
  • mem: Memory per task
  • time: Time limit
  • job_name: Job name
  • array_parallelism: Number of parallel tasks