scip-workflows 0.1.0

No project description provided

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:

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.