MPUSP Snakemake wrappers

Purpose

This repository is a collection of custom Snakemake wrappers. The Snakemake community maintains a wide variety of Wrappers for recurring tasks in the life sciences.

A wrapper is simply a standardized script with a pinned software environment that can be re-used in existing workflows. Wrappers often simply provide a reproducible interface to existing tools. How wrappers work is covered in detail on the Snakemake Docs and the Snakemake Wrapper Homepage

Use wrappers in a project

Wrappers can be included in any workflow using the wrapper directive instead of script or shell. This is an example for using the GFFCOMPARE wrapper. Note that a GitHub URL needs to be provided that points to the raw.githubusercontent.com destination of a wrapper, not the rendered HTML.

rule test_gffcompare:
    input:
        gff=["file1.gff", "file2.gff", "file3.gff"],
        # optional input files
        # reference="", # reference transcriptome in GFF/GTF format
        # fasta="", # reference genome sequence in FASTA format
    output:
        # it is recommended to use the `multiext` statement, as all output files are
        # created using a common prefix
        multiext("gffcmp", ".combined.gtf", ".loci", ".stats", ".tracking"),
    threads: 1
    log:
        "logs/gffcompare.log",
    params:
        # To combine features from all GFF input files without redundancy, use `-C`
        extra="-C",
    wrapper:
        "https://raw.githubusercontent.com/MPUSP/mpusp-snakemake-wrappers/refs/heads/main/gffcompare"

Adding wrappers to this repository

Wrappers that are to be added to this repository shoul already follow the standards of the official Snakemake wrapper repository. This way it will be easy to transfer them to the official wrapper collection if desired.

To add a wrapper, create a new directory named according to your tool, and add:

• <your_tool>/wrapper.py -- the wrapper script, can be a python or R script
• <your_tool>/environment.yaml -- the conda env definition
• <your_tool>/environment.linux-64.pin.txt -- the pinned env, for exact reproduction
• <your_tool>/meta.yaml -- desciption of the tool, its, purpose, authors, parameters, etc
• <your_tool>/test -- A real-world test case, see the official snakemake wrappers documentation

Tests are automatically run on wrappers if wrappers have a valid directory structure. This means they need to have a wrapper.py and a test sub-directory as main content.

License

• Wrappers in this repository are MIT-licensed
• Note: all wrapped/external software is licensed under its own terms
• Wrappers only provide an interface to call external software using the Snakemake workflow manager