Welcome to the snakemake wrapper documentation from Loosolab!¶

This repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows.

Usage¶

The general strategy is to include a wrapper into your workflow via the wrapper directive, e.g.

rule samtools_sort:
    input:
        "mapped/{sample}.bam"
    output:
        "mapped/{sample}.sorted.bam"
    params:
        "-m 4G"
    threads: 8
    wrapper:
        "samtools/sort"

To automatically download the corresponding wrapper from the repository, just add --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/ to your Snakemake call.

Each wrapper defines required software packages and versions. In combination with the --use-conda flag of Snakemake, these will be deployed automatically.

Contribute¶

provide a meta.yaml with name, description and author of the wrapper,
provide an environment.yaml which lists all required software packages (the packages shall be available via https://anaconda.org),
follow the python style guide,
use 4 spaces for indentation.