{"id":24244269,"url":"https://github.com/sk-sahu/snakeflows","last_synced_at":"2025-04-14T11:38:34.597Z","repository":{"id":34244866,"uuid":"171293144","full_name":"sk-sahu/Snakeflows","owner":"sk-sahu","description":"Collective Snakemake workflows for easy and reproducible NGS data analysis.","archived":false,"fork":false,"pushed_at":"2023-08-05T13:54:53.000Z","size":312,"stargazers_count":5,"open_issues_count":12,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-14T22:03:53.808Z","etag":null,"topics":["rna-seq-analysis","snakemake-workflows"],"latest_commit_sha":null,"homepage":"https://sksahu.net/Snakeflows","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sk-sahu.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-02-18T13:53:14.000Z","updated_at":"2023-08-05T13:53:54.000Z","dependencies_parsed_at":"2023-01-15T05:46:17.228Z","dependency_job_id":null,"html_url":"https://github.com/sk-sahu/Snakeflows","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sk-sahu%2FSnakeflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sk-sahu%2FSnakeflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sk-sahu%2FSnakeflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sk-sahu%2FSnakeflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sk-sahu","download_url":"https://codeload.github.com/sk-sahu/Snakeflows/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248873044,"owners_count":21175548,"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":["rna-seq-analysis","snakemake-workflows"],"created_at":"2025-01-14T22:04:37.468Z","updated_at":"2025-04-14T11:38:34.550Z","avatar_url":"https://github.com/sk-sahu.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Snakeflows\n\n[![Snakemake](https://img.shields.io/badge/snakemake-≥5.2.3-blueviolet.svg)](https://snakemake.readthedocs.io/en/stable/)\n[![Documentation Status](https://readthedocs.org/projects/snakemake-rnaseq-workflows/badge/?version=latest)](https://snakemake-rnaseq-workflows.readthedocs.io/en/latest/?badge=latest)\n\n**Collective Snakemake workflows for easy and reproducable NGS data analysis.**\n\nWorkflows may contain modified parameters, Please look at `snakemake` files before use.\n\n### RNA-Seq Analysis\nCurrct workflows\n* [STAR-Cufflinks](./STAR-Cufflinks)\n* [Salmon](./Salmon)\n\nWorkflows are making in progress. I will add more downstreem tools as go along.\nYou have an workflow in mind too add! Requet it here - [![feature](https://img.shields.io/badge/Issue-Feature_request-orange.svg)](https://github.com/sk-sahu/Snakemake-RNASeq-Workflows/issues/new?assignees=\u0026labels=\u0026template=feature_request.md\u0026title=)\n\n### Quick start\n\n#### Pre-requirements\nYou need to have [Python3](https://www.python.org/downloads/release/python-356/) installed in your system with `conda` enabled.\n\nInstall needed tools with following command\n```bash\nconda env create -f environment.yml\nconda activate snakeflows\n```\n\nDownlorad sample data to test the workflow:\n```\nwget https://www.dropbox.com/s/bnvjbhq4970pvg8/sample_data.tar.gz?dl=0\n```\n\n#### 1. Prepare **samples** directory properly\n\nBefore you run `write_sample_to_json.py`, **samples** directory arangement and it's naming needs to be proper such that it can be read by the script and call furthere in `snakemake` files.\n\nSomething like this:\n```\nsamples\n├── SET1_dummy\n│   ├── SET1_dummy_R1.fastq.gz\n│   └── SET1_dummy_R2.fastq.gz\n└── SET3_dummy\n    ├── SET3_dummy_R1.fastq.gz\n    └── SET3_dummy_R2.fastq.gz\n```\n\n#### 2. Generate `samples.json` file\nThis will be used to automatic detect samples names and call them in `snakemake` files.\n```bash\npython3 write_sample_to_json.py --fastq_dir full_path_to_samples_directory\n```\n\n#### 3. Run Workflows\nFirst Edit the `config.yml` files inside workflow directory with required full paths.\n\nThen simply call `snakemake` from workflow directory (With additional parameters if required)\n```\nsnakemake --cores 12\n```\n#### Additional\nFor checking workflow and debug\n```bash\nsnakemake -np\n```\n\nVisualise the workflow\n```bash\nsnakemake --forceall --dag | dot -Tpng | display\n```\n\nUpcoming additons:\n* Docker integration ![Docker Cloud Automated build](https://img.shields.io/docker/cloud/automated/sangramkeshari/snakeflows.svg) \n![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/sangramkeshari/snakeflows.svg)\n* Streamlined html reports\n* Log files with timestamp\n* Making it more modular with .smk files\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsk-sahu%2Fsnakeflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsk-sahu%2Fsnakeflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsk-sahu%2Fsnakeflows/lists"}