check-my-sample-sheet 1.0.0

Streamlit web application to validate Illumina sample sheets (bcl2fastq v1 and BCL Convert v2).

Check My Sample Sheet

This is a streamlit application that uses Sequana (github.com/sequana/sequana) iem modules to check Sample Sheets from Illumina sequencers. Both formats are supported and detected automatically:

• v1 (bcl2fastq): [Data] / [Settings] sections
• v2 (BCL Convert): [BCLConvert_Data] / [BCLConvert_Settings] sections

Running demo is here: https://check-my-sample-sheet.streamlit.app/

General Information

If you want to contribute to this web application, please provide PR here. Note, however, that the core of the application is within the Sequana project on https://github.com/sequana/sequana/, more specifically in the iem.py module.

The sanity checks implemented are based on experience, the bcl2fastq documentation (v2.20) and the BCL Convert specification.

Installation

From PyPI:

pip install check-my-sample-sheet

Then launch the app (opens in your browser); extra arguments are forwarded to streamlit run (e.g. --server.port 8502):

check-my-sample-sheet

Local instance (from source)

git clone https://github.com/sequana/webapp_samplesheet
cd webapp_samplesheet

# install the dependencies (sequana, streamlit, ...)
pip install -r requirements.txt

# run the application locally in your browser
streamlit run check_my_sample_sheet/app.py

Running the tests

pip install -r requirements-dev.txt
pytest