intelliseq-iflow

CLI tool for iFlow - genomic data management and workflow execution.

Installation

pip install intelliseq-iflow

Usage

Authentication

Login using OAuth Device Flow:

iflow login

This will open a browser for authentication. Your credentials are stored securely in your system keyring.

Check login status:

iflow status

Logout:

iflow logout

File Operations

List files in a project:

iflow files ls --project PROJECT_ID
iflow files ls --project PROJECT_ID --path data/raw/

Download a file:

iflow files download --project PROJECT_ID --path data/file.txt
iflow files download --project PROJECT_ID --path data/file.txt -o local_file.txt

Upload a file:

iflow files upload --project PROJECT_ID local_file.txt data/uploaded.txt

Running Pipelines

Submit a pipeline run:

iflow runs submit --pipeline hereditary-mock \
  -P case_id=patient-001 \
  -P child_fastq=data/R1.fastq.gz \
  --watch

With LIS callback:

iflow runs submit --pipeline hereditary-panel \
  -P vcf_file=data/sample.vcf.gz \
  --callback-url https://lis.example.com/api/callback

Configuration

Configure environment:

iflow config env dev    # Development
iflow config env stg    # Staging
iflow config env prod   # Production

Select default project:

iflow config select-project

View current configuration:

iflow config show

Development

# Install in development mode
pip install -e ".[dev]"

# Run tests
pytest

# Format code
ruff format .
ruff check --fix .