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The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows.
The general strategy is to include a wrapper into your workflow via the wrapper directive, e.g.
Each wrapper defines required software packages and versions in an environment.yaml file. In combination with the --use-conda flag of Snakemake, this will be deployed automatically.
Alternatively, for example for development, the wrapper directive can also point to full URLs, including the local file://. For this to work, you need to provide the (remote) path to the directory containing the wrapper.* and environment.yaml files. For the above example, the explicit GitHub URL to specify would need to be the /raw/ version of the directory:
rule samtools_sort: input: "mapped/{sample}.bam" output: "mapped/{sample}.sorted.bam" params: "-m 4G" threads: 8 wrapper: "https://github.com/snakemake/snakemake-wrappers/raw/0.2.0/bio/samtools/sort"
We invite anybody to contribute to the Snakemake Wrapper Repository. If you want to contribute refer to the contributing guide.