https://github.com/solida-core/astra
Snakemake pipeline to performs Variant Calling (with DeepVariant) and Variant Annotation (with VEP) starting from tumor BAM files.
https://github.com/solida-core/astra
Last synced: 12 months ago
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Snakemake pipeline to performs Variant Calling (with DeepVariant) and Variant Annotation (with VEP) starting from tumor BAM files.
- Host: GitHub
- URL: https://github.com/solida-core/astra
- Owner: solida-core
- License: gpl-3.0
- Created: 2024-10-25T13:10:03.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-11-21T15:22:31.000Z (over 1 year ago)
- Last Synced: 2024-12-27T20:46:12.896Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 179 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Snakemake workflow: ASTRA
[](https://snakemake.bitbucket.io)
ASTRA (Advanced Snakemake Pipeline for Thorough Variant Analysis) performs
Variant Calling (with [DeepVariant](https://github.com/google/deepvariant)) and
Variant Annotation (with [VEP](https://grch37.ensembl.org/info/docs/tools/vep/index.html))
starting from tumor BAM files.
ASTRA is part of the Snakemake-based pipelines collection [solida-core](https://github.com/solida-core)
developed and manteined at [CRS4](https://www.crs4.it).
## Authors
* Rossano Atzeni ([@ratzeni](https://github.com/ratzeni))
* Riccardo Berutti ([@berutti](https://github.com/berutti))
## Usage
The usage of this workflow is described in the
[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=solida-core/astra).
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:
```commandline
mamba create -c bioconda -c conda-forge --name snakemake snakemake=8.25 apptainer=1.3.0 snakedeploy
```
Activate the environment with:
```commandline
conda activate snakemake
```
### Installation of Optional Prerequisites
The following prerequisites are optional and may be installed based on your workflow requirements:
```bash
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](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/) 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:
```bash
snakedeploy deploy-workflow https://github.com/solida-core/astra \
/path/to/my_work_dir \
--branch master # or use --tag
```
### 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](./config/README.md) 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:
```bash
snakemake --use-conda -p --cores all
```
### Generating a Report
To create a comprehensive analysis report, use the command:
```bash
snakemake --report report.zip --cores all
```