This profile configures Snakemake to run on the SLURM Workload Manager with modifications to suit users of SCG in the Bhatt lab.

To deploy this profile, run

mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
pip install cookiecutter
cookiecutter https://github.com/bhattlab/slurm.git

Then, you can run Snakemake with

snakemake --profile scg ...

The following resources are supported by on a per-rule basis:

• mem: set the memory resource request in mb.
• walltime, runtime: set the time resource in min.
• ntasks: set the number of cpus

Example rule that defines resource requirements:

rule bwa_align:
	input: "in"
	output: "out"
	resources:
		mem=32,
		time=48
	threads: 24
	shell: "do something"

Test-driven development is enabled through the tests folder. Provided that the user has installed docker and enabled docker swarm, the SLURM tests will download two images:

1. quay.io/biocontainers/snakemake
2. giovtorres/docker-centos7-slurm

In addition, testing of the cookiecutter template itself is enabled through the pytest plugin for Cookiecutters. You can run the tests by issuing

pytest -v -s