Customizing Snakemake Wrappers

(This is WIP)

Thanks to Tessa Pierce and Taylor Reiter from the DIB lab for helping with this!

In my latest variant discovery work, I found myself grappling with Snakemake wrappers. I needed to run many vcf files through GATK’s GenomicsDBImport (v4.1.9.0)

Here is a usage example for GenomicsDBImport provided on the official webpage

gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \
  -V data/gvcfs/mother.g.vcf.gz \
  -V data/gvcfs/father.g.vcf.gz \
  -V data/gvcfs/son.g.vcf.gz \
  --genomicsdb-workspace-path my_database \
  --tmp-dir=/path/to/large/tmp \
  -L 20

As you can see, I need a -V flag in front of each vcf.gz file being processed. To pass all my vcf files through this command, I would have to write a little bash script. That’s not great for me.

Thankfully, there’s a neat little Snakemake wrapper for this:

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"

rule genomics_db_import:
    input:
        gvcfs=["calls/a.g.vcf.gz", "calls/b.g.vcf.gz"],
    output:
        db=directory("db"),
    log:
        "logs/gatk/genomicsdbimport.log"
    params:
        intervals="ref",
        db_action="create", # optional
        extra="",  # optional
        java_opts="",  # optional
    resources:
        mem_mb=1024
    wrapper:
        "0.77.0/bio/gatk/genomicsdbimport"

My problem is that this wrapper calls GATK version 4.2.0.0. And I need version 4.1.9.0.

Turns out that there’s no good documentation or resource for wrapper version shifts. The easiest way to get the version of a software you want, is to customize the wrapper script.

This is a mini tutorial on how to customize the version of GenomicsDBImport in a pre-written wrapper.

Step 1: Download and save the wrapper

I copied the code into a text editor and saved it with a .py extension. The script for the GenimicsDBImport lives here

Step 2: Download and edit the environment.yml

I copied the environment.yml from the GitHub repo, pasted it into a text file and saved it to environment.yml extension. Then changed the version of GATK like shown here:

channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - gatk4 ==4.1.9.0
  - snakemake-wrapper-utils ==0.1.3

Step 3: Replace Wrapper

In my Snakefile, I replaced the wrapper: /path/to/wrapper directive with:

script: /path/name-of-wrapper.py
conda: /path/this-version.environment.yml

And that should work!