Snakemake workflow: ASTRA

ASTRA (Advanced Snakemake Pipeline for Thorough Variant Analysis) performs Variant Calling (with DeepVariant) and Variant Annotation (with VEP) starting from tumor BAM files. ASTRA is part of the Snakemake-based pipelines collection solida-core developed and manteined at CRS4.

Authors

• Rossano Atzeni (@ratzeni)
• Riccardo Berutti (@berutti)

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

Quick Start

Creating the Conda Environment

To create a virtual environment, use the following command:

mamba create -c bioconda -c conda-forge --name snakemake snakemake=8.25 apptainer=1.3.0 snakedeploy

Activate the environment with:

conda activate snakemake

Installation of Optional Prerequisites

The following prerequisites are optional and may be installed based on your workflow requirements:

mamba install snakemake-executor-plugin-drmaa=0.1.5  # Optional: For DRMAA cluster execution. Replace with your preferred Snakemake executor plugin (see: https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/).
mamba install yq=3.4.3  # Optional: Required only if you plan to use the launcher `run.astra.sh`.

Notes:

• Snakemake Executor Plugins: The snakemake-executor-plugin-drmaa plugin is an example for DRMAA cluster execution. You can replace it with another executor plugin of your choice. See the Snakemake Plugin Catalog for available options.
• yq: This tool is needed only if you plan to use the run.astra.sh launcher script, which simplifies execution and configuration.

Deployment of Astra

Deploy the pipeline by specifying an output directory my_work_dir and a pipeline tag or branch:

snakedeploy deploy-workflow https://github.com/solida-core/astra \
                            /path/to/my_work_dir \
                            --branch master  # or use --tag <version>

Running Astra

Before running the pipeline, ensure that you edit the configuration files located in the ./config/ directory:

• config.yaml: Main configuration file for setting pipeline parameters.
• samples.tsv: A table listing the samples included in the analysis.
• units.tsv: Details about the technical units associated with each sample.
• reheader.tsv: Optional file for reheadering sample identifiers.

Refer to the Configuration Details section for a comprehensive guide on editing these files.

Once the configuration files are correctly set up, navigate to the deployed pipeline directory and execute the pipeline with:

snakemake --use-conda -p --cores all

Generating a Report

To create a comprehensive analysis report, use the command:

snakemake --report report.zip --cores all