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 0.3.20
File	Size	Uploaded
intelliseq_iflow-0.3.20.tar.gz	55.8 kB	Sep 21, 2026	Details

Table of built distributions (wheels) for intelliseq-iflow 0.3.20
File	Interpreter	ABI	Platform	Reset
intelliseq_iflow-0.3.20-py3-none-any.whl 58.1 kB Sep 21, 2026	Python 3	none	any	Details

Total release size: 113.8 kB

Download URL	intelliseq_iflow-0.3.20.tar.gz
Size	55.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`a271f1698470b26d3d75102a82a94b757683bdcdd79c8599b7383198c286575e`
BLAKE2b-256 checksum How to use checksums	`1eb5fb2ab9f374a66afc90a0533b1b2eb0d6f625ac4a7829a920eb77e78fa9bf`
Upload date	Sep 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`

Download URL	intelliseq_iflow-0.3.20-py3-none-any.whl
Size	58.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`8bdc42db6660dd2e9b9372cea07d4ac5d37d4e1cf3728b7cd400d48ee24738e1`
BLAKE2b-256 checksum How to use checksums	`01873fb385bcf79ca7d6abd71bdc58c531f7f97a6dc00509275722d3e31bd894`
Upload date	Sep 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.3`