Snakemake workflow for running the Better Base Quality (BBQ) tool for somatic variant calling.
The usage of this workflow is also described in the Snakemake Workflow Catalog.
Snakemake is best to be installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it can be installed via Mambaforge. For other options see here.
Given that Mamba is installed, run:
mamba create -c conda-forge -c bioconda --name snakemake 'snakemake>=8'
to install Snakemake in an isolated environment. If you need to use conda instead of mamba, --conda-frontend conda flag needs to be added to the snakemake commands given below.
Activate the environment via:
conda activate snakemake
Download and extract the repository:
git clone https://github.com/BesenbacherLab/bbq_pipeline.git && cd bbq_pipeline
To specify the parameters for running BBQ, reference genome and sample paths, modify the configuration files config.yaml and samples.tsv according to your needs, following the explanations provided here.
The source code and instructions for running BBQ can be found on the BBQ github page.
For cluster execution of the workflow, the snakemake slurm executor plugin needs to be installed with pip install snakemake-executor-plugin-slurm. If the slurm plugin is not installed, the -e flag needs to be specified for the snakemake commands listed below.
The specifics for cluster execution should be defined in the workflow profile configuration file. An example workflow profile for slurm is provided here. To use the example profile, adjust the snakemake command line parameters to your needs. Importantly, a cluster account is specified in the example profile as an environment variable. To set the account name as an environment variable run export ACCOUNT_NAME=<your_account_name> or modify the profile config file to include your account name directly.
After you have activated the conda environment with snakemake, installed the slurm executor plugin and set the account name as an environment variable, you can test the workflow remote execution by performing a dry-run:
snakemake -n
To run the workflow for a new data set, use the --directory flag that specifies the path to the directory where the pipeline will be executed. The target directory needs to include a config folder with config.yaml and samples.tsv files, which specify the BBQ parameters, reference genome and paths to sample files that will be used during execution. You can execute the workflow with:
snakemake --directory "path/to/new/directory/"
To run the workflow with the provided test data in the .test folder run:
snakemake --directory ".test"
The workflow profile that specifies the details for the cluster execution will be still automatically detected from the pipeline directory (workflow/profiles/default/config.yaml) even when the execution directory is changed. If you want to specify a new cluster execution profile as well, use the --workflow-profile flag:
snakemake --workflow-profile "path/to/workflow_profile/config.yaml"
For further options for local, cluster and cloud execution, see the snakemake docs.
After running the workflow, you can automatically generate an HTML report with an overview of the results via:
snakemake --report report.html