1. Johannes Köster
  2. Snakemake Workflows

Overview

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Snakemake

The Snakemake Workflow Repository

The Snakemake Workflow Repository is a collection of reusable and modularized Snakemake rules and workflows. The provided code should also serve as a best-practices guide of how to build production ready workflows with Snakemake.

Structure

Rules can be found under

<discipline>/<subject>/rules/<analysis_step>/<name>.rules

The general strategy is to include these into your workflow via the include directive. This can also happen via https urls (in this case make sure, that you trust the source). Example workflows following this strategy can be found under::

<discipline>/<subject>/workflows/<name>/Snakefile

Content

Next Generation Sequencing

So far, this repository contains rules for the read mappers BWA and PEANUT, general samtools rules for manipulating SAM/BAM files, rules for the variant callers GATK and Freebayes and two example variant calling workflows (based on GATK and Freebayes).

Contribute

We invite anybody to contribute to the Snakemake Workflow Repository. If you want to contribute we suggest the following procedure:

  • fork the repository
  • develop your contribution
  • perform a pull request

The pull request will be reviewed and included as fast as possible. Thereby, contributions should follow the coding style of the already present examples, i.e.

  • start with a docstring describing the usage and purpose,
  • define author with email address and a license,
  • follow the python style guide,
  • be customizable via a json config file parsed into a variable CONFIG,
  • use 4 spaces for indentation,
  • specify reasonable default values for threads and resources.