sinanugur/cellsnake repository overview

⁠Cellsnake

Official Docker repo of cellsnake workflow.

The project's GitHub https://github.com/sinanugur/cellsnake⁠.

Our documentation https://cellsnake.readthedocs.io/en/latest/⁠.

or here https://zenodo.org/record/7919631/files/fetal-brain-data.zip?download=1⁠

⁠Quick start example

For example start a run with default settings, and assume data/ folder contains input files, a standard run:

docker run  -it --rm -v "$(pwd):/app" sinanugur/cellsnake:latest cellsnake standard data 

to print help

docker run  -it --rm -v "$(pwd):/app" sinanugur/cellsnake:latest cellsnake --help

⁠Using Podman

You may use Podman as an alternative.

podman pull sinanugur/cellsnake
podman run  -it --rm -v "$(pwd):/app" sinanugur/cellsnake:latest cellsnake --help

⁠Changelog

0.2.0.12 version. Bioconda version is missing. Available on PyPi. Minor fixes. Feb 2024.

0.2.0.11 version, also available on Bioconda. Available on PyPi. Some minor bug fixes for visualization issues and some fixes for metagenome analysis. 14 Aug 2023

0.2.0.1 version, not available on Bioconda yet due to a bug on Bioconda. Available on PyPi. Some minor bug fixes for performance and memory issues. 24 May 2023

0.2.0.1 version is now the latest, not available on Bioconda yet. Some minor bug fixes. 22 May 2023

0.2.0 version had a bug on Celltypist, please pull the new version. 16 May 2023.