{"id":20752812,"url":"https://github.com/fritzbayer/snakemake-with-r","last_synced_at":"2025-09-27T21:32:05.266Z","repository":{"id":51769015,"uuid":"470255410","full_name":"fritzbayer/snakemake-with-R","owner":"fritzbayer","description":"Simple template for running snakemake with R","archived":false,"fork":false,"pushed_at":"2023-01-31T12:12:55.000Z","size":36,"stargazers_count":11,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-09T10:45:30.713Z","etag":null,"topics":["r-workflow","snakemake","snakemake-pipeline","snakemake-workflow"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fritzbayer.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-03-15T17:01:47.000Z","updated_at":"2025-02-01T21:13:36.000Z","dependencies_parsed_at":"2023-02-16T18:55:35.406Z","dependency_job_id":null,"html_url":"https://github.com/fritzbayer/snakemake-with-R","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/fritzbayer/snakemake-with-R","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzbayer%2Fsnakemake-with-R","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzbayer%2Fsnakemake-with-R/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzbayer%2Fsnakemake-with-R/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzbayer%2Fsnakemake-with-R/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fritzbayer","download_url":"https://codeload.github.com/fritzbayer/snakemake-with-R/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzbayer%2Fsnakemake-with-R/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":277295918,"owners_count":25794402,"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","status":"online","status_checked_at":"2025-09-27T02:00:08.978Z","response_time":73,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["r-workflow","snakemake","snakemake-pipeline","snakemake-workflow"],"created_at":"2024-11-17T08:42:45.840Z","updated_at":"2025-09-27T21:32:05.007Z","avatar_url":"https://github.com/fritzbayer.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Simple template for running snakemake with R\n\nThe following terminal commands can be used to execute this demo script. \n\nStep 1: Activate conda and snakemake\n\n```{r eval=FALSE}\n$ conda activate base\n$ conda activate snakemake\n```\n\nStep 2: Download the snakemake-with-R folder and change directory accordingly\n\n```{r eval=FALSE}\n$ cd /path/to/snakemake-with-R\n```\n\nThe folder `snakemake-with-R` contains the `Snakefile`, which contains the snakemake rules from which we can execute our R scripts. The folder `scr` contains two R scripts that show two different ways how variables can be passed between R and snakemake. The folder `data` contains a simple vector that is multiplied by the snakemake rules.\n\nStep 3: Execute R scripts in the snakemake rules\n\nFirst, you can perform a dry run of Snakemake with:\n\n```{r eval=FALSE}\n$ snakemake -n\n```\n\nFor the two different ways how variables can be passed between R and snakemake, there are two different Snakemake rules. You can execute them as follows:\n\n```{r eval=FALSE}\n$ snakemake --cores 1 simple_test_rule\n```\nor \n```{r eval=FALSE}\n$ snakemake --cores 1 test_rule\n```\n\nThe output is a simple multplication of the imput vector. \n\nFrom here, you can make your workflow arbitrarily complex - enjoy.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffritzbayer%2Fsnakemake-with-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffritzbayer%2Fsnakemake-with-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffritzbayer%2Fsnakemake-with-r/lists"}