Metadata-Version: 2.1
Name: scip-workflows
Version: 0.1.0
Home-page: https://github.com/mlippeve/ehv/tree/master/
Author: Maxim Lippeveld
Author-email: maxim.lippeveld@ugent.be
License: Apache Software License 2.0
Keywords: imaging flow cytometry bioinformatics computational biology SCIP
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# SCIP use case workflows

This repository contains Snakemake workflows to reproduce use cases presented in [insert paper].

It is built using two frameworks:
- nbdev
- Snakemake

nbdev makes is a framework for developing reusable code in notebooks. Functions are defined and
tested in notebooks, and exported to a package. This package can be installed and reused in other
notebooks or scripts.

Snakemake is a workflow framework to create reproducible data analyses. Workflows are defined
via a human-readable language, and can be easily executed in various environments.

## Installation



## Usage

The repository can be used to reproduce the use cases, or for development.

### Reproduce use cases

This involves executing the Snakemake workflows. The following expects snakemake to be available.
Snakemae can be executed using conda environments or a pre-existing environment
containing all required packages.

To reproduce a use-case, open a terminal in the current directory and execute:
```bash
snakemake --configfile config/use_case.yaml --directory root_dir
```
This expects the environment to contain all required dependencies. Add `--use-conda` to let
Snakemake create a conda environment containing all requirements.

### Development

This involves the nbdev framework.
