{"id":13593497,"url":"https://github.com/snakemake-workflows/single-cell-rna-seq","last_synced_at":"2026-01-12T07:37:04.342Z","repository":{"id":85331501,"uuid":"134401394","full_name":"snakemake-workflows/single-cell-rna-seq","owner":"snakemake-workflows","description":"A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.","archived":false,"fork":false,"pushed_at":"2022-11-22T23:36:06.000Z","size":9812,"stargazers_count":101,"open_issues_count":2,"forks_count":45,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-05-30T12:29:45.601Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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/snakemake-workflows.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}},"created_at":"2018-05-22T10:50:25.000Z","updated_at":"2025-01-16T13:16:44.000Z","dependencies_parsed_at":null,"dependency_job_id":"3b89cde9-2f23-4654-9804-7708625bff75","html_url":"https://github.com/snakemake-workflows/single-cell-rna-seq","commit_stats":null,"previous_names":[],"tags_count":2,"template":true,"template_full_name":null,"purl":"pkg:github/snakemake-workflows/single-cell-rna-seq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake-workflows%2Fsingle-cell-rna-seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake-workflows%2Fsingle-cell-rna-seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake-workflows%2Fsingle-cell-rna-seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake-workflows%2Fsingle-cell-rna-seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/snakemake-workflows","download_url":"https://codeload.github.com/snakemake-workflows/single-cell-rna-seq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake-workflows%2Fsingle-cell-rna-seq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28336582,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-12T06:09:07.588Z","status":"ssl_error","status_checked_at":"2026-01-12T06:05:18.301Z","response_time":98,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2024-08-01T16:01:20.874Z","updated_at":"2026-01-12T07:37:04.325Z","avatar_url":"https://github.com/snakemake-workflows.png","language":"R","funding_links":[],"categories":["Software packages"],"sub_categories":["Other applications"],"readme":"# Snakemake workflow: single-cell-rna-seq\n\n[![Snakemake](https://img.shields.io/badge/snakemake-≥5.1.4-brightgreen.svg)](https://snakemake.readthedocs.io)\n[![GitHub actions status](https://github.com/snakemake-workflows/single-cell-rna-seq/workflows/Tests/badge.svg?branch=master)](https://github.com/snakemake-workflows/single-cell-rna-seq/actions?query=branch%3Amaster+workflow%3ATests)\n[![Snakemake-Report](https://img.shields.io/badge/snakemake-report-green.svg)](https://koesterlab.github.io/resources/snakemake-workflows/single-cell-rna-seq/report.html)\n\nA single cell RNA-seq workflow following [Lun, McCarthy and Marioni 2016](https://f1000research.com/articles/5-2122/v2) and [Soneson and Robinson 2018](https://doi.org/10.1038/nmeth.4612), with added more recent functionality.\n\n## Authors\n\n* Johannes Köster, https://koesterlab.github.io\n\n## Usage\n\nIn any case, 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, if already available, its DOI (see above).\n\n\n#### Step 1: Obtain a copy of this workflow\n\n1. Create a new github repository using this workflow [as a template](https://help.github.com/en/articles/creating-a-repository-from-a-template).\n2. [Clone](https://help.github.com/en/articles/cloning-a-repository) the newly created repository to your local system, into the place where you want to perform the data analysis.\n\n#### Step 2: Configure workflow\n\nConfigure the workflow according to your needs via editing the file `config.yaml`.\n\n#### Step 3: Execute workflow\n\nTest your configuration by performing a dry-run via\n\n    snakemake --use-conda -n\n\nExecute the workflow locally via\n\n    snakemake --use-conda --cores $N\n\nusing `$N` cores or run it in a cluster environment via\n\n    snakemake --use-conda --cluster qsub --jobs 100\n\nor\n\n    snakemake --use-conda --drmaa --jobs 100\n\nIf you not only want to fix the software stack but also the underlying OS, use\n\n    snakemake --use-conda --use-singularity\n\nin combination with any of the modes above.\nSee the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details.\n\n#### Step 4: Investigate results\n\nAfter successful execution, you can create a self-contained interactive HTML report with all results via:\n\n    snakemake --report report.html\n\nThis report can, e.g., be forwarded to your collaborators.\nAn example (using some trivial test data) can be seen [here](https://koesterlab.github.io/resources/snakemake-workflows/single-cell-rna-seq/report.html).\n\n#### Step 5: Commit changes\n\nWhenever you change something, don't forget to commit the changes back to your github copy of the repository:\n\n    git commit -a\n    git push\n\n\n#### Step 6: Obtain updates from upstream\n\nWhenever you want to synchronize your workflow copy with new developments from upstream, do the following.\n\n1. Once, register the upstream repository in your local copy: `git remote add -f upstream git@github.com:snakemake-workflows/single-cell-rna-seq.git` or `git remote add -f upstream https://github.com/snakemake-workflows/single-cell-rna-seq.git` if you do not have setup ssh keys.\n2. Update the upstream version: `git fetch upstream`.\n3. Create a diff with the current version: `git diff HEAD upstream/master workflow \u003e upstream-changes.diff`.\n4. Investigate the changes: `vim upstream-changes.diff`.\n5. Apply the modified diff via: `git apply upstream-changes.diff`.\n6. Carefully check whether you need to update the config files: `git diff HEAD upstream/master config`. If so, do it manually, and only where necessary, since you would otherwise likely overwrite your settings and samples.\n\n#### Step 7: Contribute back\n\nIn case you have also changed or added steps, please consider contributing them back to the original repository:\n\n1. [Fork](https://help.github.com/en/articles/fork-a-repo) the original repo to a personal or lab account.\n2. [Clone](https://help.github.com/en/articles/cloning-a-repository) the fork to your local system, to a different place than where you ran your analysis.\n3. Copy the modified files from your analysis to the clone of your fork, e.g., `cp -r workflow path/to/fork`. Make sure to **not** accidentally copy config file contents or sample sheets. Instead, manually update the example config files if necessary.\n4. Commit and push your changes to your fork.\n5. Create a [pull request](https://help.github.com/en/articles/creating-a-pull-request) against the original repository.\n\n## Testing\n\nTest cases are in the subfolder `.test`. They are automtically executed via continuous integration with Travis CI.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake-workflows%2Fsingle-cell-rna-seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnakemake-workflows%2Fsingle-cell-rna-seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake-workflows%2Fsingle-cell-rna-seq/lists"}