intelliseq-iflow

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

Installation

pip install intelliseq-iflow

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

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

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

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

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

# Run tests
pytest

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

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution for intelliseq-iflow 0.3.21
File	Size	Uploaded
intelliseq_iflow-0.3.21.tar.gz	61.0 kB	Sep 23, 2026	Details

Table of built distributions (wheels) for intelliseq-iflow 0.3.21
File	Interpreter	ABI	Platform	Reset
intelliseq_iflow-0.3.21-py3-none-any.whl 60.0 kB Sep 23, 2026	Python 3	none	any	Details

Total release size: 121.0 kB

Download URL	intelliseq_iflow-0.3.21.tar.gz
Size	61.0 kB
Tags	Source
SHA-256 checksum How to use checksums	`2582db3db9eafb819e62d91d0d507c8930a723c544bbff5dc11f1cc2ddcf839a`
BLAKE2b-256 checksum How to use checksums	`7dd5b3a327f8088dd44aa0892427573f5821ddb4dfad7c5216074c09d0b18589`
Upload date	Sep 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`

Download URL	intelliseq_iflow-0.3.21-py3-none-any.whl
Size	60.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`53b615e5434dd0f67d34539a9865a0d456ba88b8135d4759281ea370143d17a3`
BLAKE2b-256 checksum How to use checksums	`66e984122897165dd314b188b6184b33de5b37faac0e485991d3825bdb03e8c7`
Upload date	Sep 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`