{"id":18676534,"url":"https://github.com/solida-core/astra","last_synced_at":"2025-06-15T08:33:46.642Z","repository":{"id":259850281,"uuid":"878473985","full_name":"solida-core/astra","owner":"solida-core","description":"Snakemake pipeline to performs  Variant Calling (with DeepVariant) and  Variant Annotation (with VEP) starting from tumor BAM files.","archived":false,"fork":false,"pushed_at":"2024-11-21T15:22:31.000Z","size":183,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-27T20:46:12.896Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/solida-core.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-25T13:10:03.000Z","updated_at":"2024-11-21T15:22:35.000Z","dependencies_parsed_at":"2024-11-21T16:26:15.974Z","dependency_job_id":"59a5e891-5298-4fa1-98b6-2227cfc01cbe","html_url":"https://github.com/solida-core/astra","commit_stats":null,"previous_names":["solida-core/astra"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fastra","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fastra/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fastra/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fastra/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/solida-core","download_url":"https://codeload.github.com/solida-core/astra/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239520734,"owners_count":19652747,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T09:29:37.614Z","updated_at":"2025-02-18T17:46:07.965Z","avatar_url":"https://github.com/solida-core.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Snakemake workflow: ASTRA\n[![Snakemake](https://img.shields.io/badge/snakemake-≥8.10.0-brightgreen.svg)](https://snakemake.bitbucket.io)\n\nASTRA (Advanced Snakemake Pipeline for Thorough Variant Analysis) performs \nVariant Calling (with [DeepVariant](https://github.com/google/deepvariant)) and \nVariant Annotation (with [VEP](https://grch37.ensembl.org/info/docs/tools/vep/index.html))\nstarting from tumor BAM files.\nASTRA is part of the Snakemake-based pipelines collection [solida-core](https://github.com/solida-core) \ndeveloped and manteined at [CRS4](https://www.crs4.it). \n\u003cp align=\"center\"\u003e\n\u003cimg align=\"center\" src=\"https://www.crs4.it/wp-content/uploads/2020/11/CRS4-1.jpg\" width=\"200\" height=\"80\" alt=\"www.crs4.it\"/\u003e\n\u003c/p\u003e\n\n## Authors\n\n* Rossano Atzeni ([@ratzeni](https://github.com/ratzeni))\n* Riccardo Berutti ([@berutti](https://github.com/berutti))\n\n## Usage\n\nThe usage of this workflow is described in the \n[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=solida-core/astra).\n\nIf you use this workflow in a paper, \ndon't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).\n\n## Quick Start\n\n### Creating the Conda Environment\nTo create a virtual environment, use the following command:\n\n```commandline\nmamba create -c bioconda -c conda-forge --name snakemake snakemake=8.25 apptainer=1.3.0 snakedeploy\n```\n\nActivate the environment with:\n```commandline\nconda activate snakemake\n```\n\n### Installation of Optional Prerequisites\n\nThe following prerequisites are optional and may be installed based on your workflow requirements:\n\n```bash\nmamba 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/).\nmamba install yq=3.4.3  # Optional: Required only if you plan to use the launcher `run.astra.sh`.\n```\n\n#### Notes:\n- **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.\n- **`yq`**: This tool is needed only if you plan to use the `run.astra.sh` launcher script, which simplifies execution and configuration.\n\n### Deployment of Astra\nDeploy the pipeline by specifying an output directory `my_work_dir` and a pipeline tag or branch:\n\n```bash\nsnakedeploy deploy-workflow https://github.com/solida-core/astra \\\n                            /path/to/my_work_dir \\\n                            --branch master  # or use --tag \u003cversion\u003e\n```\n\n### Running Astra\nBefore running the pipeline, ensure that you edit the configuration files located in the `./config/` directory:\n\n- `config.yaml`: Main configuration file for setting pipeline parameters.\n- `samples.tsv`: A table listing the samples included in the analysis.\n- `units.tsv`: Details about the technical units associated with each sample.\n- `reheader.tsv`: Optional file for reheadering sample identifiers.\n\nRefer to the [Configuration Details](./config/README.md) section for a comprehensive guide on editing these files.\n\nOnce the configuration files are correctly set up, navigate to the deployed pipeline directory and execute the pipeline with:\n\n```bash\nsnakemake --use-conda -p --cores all\n```\n### Generating a Report\nTo create a comprehensive analysis report, use the command:\n\n```bash\nsnakemake --report report.zip --cores all\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fastra","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsolida-core%2Fastra","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fastra/lists"}