{"id":13586785,"url":"https://github.com/flow-r/flowr","last_synced_at":"2026-02-19T02:32:39.784Z","repository":{"id":16600388,"uuid":"19354942","full_name":"flow-r/flowr","owner":"flow-r","description":"Robust and efficient workflows using a simple language agnostic approach","archived":false,"fork":false,"pushed_at":"2025-02-14T14:53:22.000Z","size":32857,"stargazers_count":90,"open_issues_count":6,"forks_count":10,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-12-06T20:26:17.142Z","etag":null,"topics":["bioinformatics","cloud","cluster","cran","flowr","pipeline","tsv","workflow"],"latest_commit_sha":null,"homepage":"http://flow-r.github.io/flowr","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/flow-r.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2014-05-01T19:20:29.000Z","updated_at":"2025-10-06T09:15:10.000Z","dependencies_parsed_at":"2025-09-08T13:51:08.401Z","dependency_job_id":"ca106abc-0762-466a-9098-741306681d71","html_url":"https://github.com/flow-r/flowr","commit_stats":null,"previous_names":["sahilseth/flowr"],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/flow-r/flowr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flow-r%2Fflowr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flow-r%2Fflowr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flow-r%2Fflowr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flow-r%2Fflowr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/flow-r","download_url":"https://codeload.github.com/flow-r/flowr/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flow-r%2Fflowr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29601091,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-19T00:59:38.239Z","status":"online","status_checked_at":"2026-02-19T02:00:07.702Z","response_time":117,"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":["bioinformatics","cloud","cluster","cran","flowr","pipeline","tsv","workflow"],"created_at":"2024-08-01T15:05:48.565Z","updated_at":"2026-02-19T02:32:39.757Z","avatar_url":"https://github.com/flow-r.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"---\noutput: \n    html_document: \n       keep_md: yes\npackagedocs:\n    toc: false\nnavpills: |\n  \u003cli\u003e\u003ca href='docs.html'\u003eOverview\u003c/a\u003e\u003c/li\u003e\n  \u003cli\u003e\u003ca href='install.html'\u003eInstall\u003c/a\u003e\u003c/li\u003e\n  \u003cli\u003e\u003ca href='tutorial.html'\u003eTutorial\u003c/a\u003e\u003c/li\u003e\n  \u003cli\u003e\u003ca href='rd.html'\u003eHelp\u003c/a\u003e\u003c/li\u003e\n  \u003cli\u003e\u003ca href='news.html'\u003eNews\u003c/a\u003e\u003c/li\u003e\n  \u003cli\u003e\u003ca href='https://github.com/flow-r/flowr'\u003eGithub \u003ci class='fa fa-github'\u003e\u003c/i\u003e\u003c/a\u003e\u003c/li\u003e\n---\n\n\u003c!--brand: |-\n  \u003ca href=\"http://flow-r.github.io/flowr\"\u003e\n  \u003cimg src='https://raw.githubusercontent.com/sahilseth/flowr/devel/vignettes/files/logo.png' alt='flowr icon' width='40px' height='40px' style='margin-top: -10px;'\u003e\n  \u003c/a\u003e\n--\u003e\n\n  \n\u003cmeta property=\"og:description\" content=\"Easy, scalable big data pipelines using hpcc (high performance computing cluster)\"\u003e\n\u003cmeta property=\"og:title\" content=\"flowr — Easy, scalable big data pipelines using hpcc\"\u003e\n\u003cmeta name=\"twitter:description\" content=\"flowr - Easy, scalable big data pipelines using hpcc (high performance computing cluster)\"\u003e\n\u003cmeta name=\"twitter:title\" content=\"flowr — Easy, scalable big data pipelines using hpcc (high performance computing cluster)\"\u003e\n\n\n[![Build Status](https://travis-ci.org/sahilseth/flowr.svg?branch=master)](https://travis-ci.org/sahilseth/flowr)\n[![cran](http://www.r-pkg.org/badges/version/flowr)](https://cran.r-project.org/package=flowr)\n\u003c!--[![codecov.io](http://codecov.io/github/sahilseth/flowr/coverage.svg?branch=devel)](http://codecov.io/github/sahilseth/flowr?branch=devel)--\u003e\n![downloads](http://cranlogs.r-pkg.org/badges/grand-total/flowr)\n\n\u003c!--\n![license](https://img.shields.io/badge/license-MIT-blue.svg)\n--\u003e\n\n\n## [![flow-r.github.io/flowr](https://raw.githubusercontent.com/sahilseth/flowr/devel/vignettes/files/logo.png) Streamlining Computing workflows](http://flow-r.github.io/flowr/)\n\n**Latest documentation: [flow-r.github.io/flowr](http://flow-r.github.io/flowr/)**\n\n\n\nFlowr framework allows you to design and implement complex pipelines, and\ndeploy them on your institution's computing cluster. This has been built\nkeeping in mind the needs of bioinformatics workflows. However, it is\neasily extendable to any field where a series of steps (shell commands)\nare to be executed in a (work)flow.\n\n### Highlights\n\n- No new **syntax or language**. Put all shell commands as a tsv file called [flow mat](http://flow-r.github.io/flowr/overview.html#flow_matrix).\n- Define the [flow of steps](http://flow-r.github.io/flowr/overview.html#relationships) using a simple tsv file (serial, scatter, gather, burst...) called [flow def](http://flow-r.github.io/flowr/overview.html#flow_definition).\n- Works on your laptop/server or cluster (/cloud).\n- Supports **multiple cluster computing platforms** (torque, lsf, sge, slurm ...), cloud (star cluster) OR a local machine.\n- One line installation (`install.packages(\"flowr\")`)\n- **Reproducible** and **transparent**, with cleanly structured execution logs\n- **Track** and **re-run** flows\n- **Lean** and **Portable**, with easy installation\n- **Fine grain** control over resources (CPU, memory, walltime, etc.) of each step.\n\n### Example\n[![ex_fq_bam](http://flow-r.github.io/flowr/files/ex_fq_bam.png)](https://github.com/flow-r/fastq_bam)\n\n\u003c!---\n- Example: \n\t- A typical case in next-generation sequencing involves processing of tens of\n   [fastqs](http://en.wikipedia.org/wiki/FASTQ_format) for a sample,\n   [mapping](http://en.wikipedia.org/wiki/Sequence_alignment) them to a reference genome.\n\t- Each step requires a range resources in terms of CPU, RAM etc.\n\t- Consider step 1 uses 10 cores for each file; with 50 files it would use 500 cores in total.\n\t- Next step uses one core for each file, 50 cores in total.\n\t- Say step C merges them, and uses only 1 core.\n\t- Some pipelines may reserve the maximum, example say 500 cores throught steps 1 to 3, \n\tflowr would handle the **surge**, reserving 500, 50 or 1; when needed.\n\t- Now consider the run has 10 samples, all of them would be procesed in\n\t parallel, spawning **thousands of cores**.\n---\u003e\n\n\n### A few lines, to get started\n\n``` {r, eval=FALSE}\n## Official stable release from CRAN (updated every other month)\n## visit flow-r.github.io/flowr/install for more details\ninstall.packages(\"flowr\",  repos = \"http://cran.rstudio.com\")\n\n# or a latest version from DRAT, provide cran for dependencies\ninstall.packages(\"flowr\", repos = c(CRAN=\"http://cran.rstudio.com\", DRAT=\"http://sahilseth.github.io/drat\"))\n\nlibrary(flowr) ## load the library\nsetup() ## copy flowr bash script; and create a folder flowr under home.\n\n# Run an example pipeline\n\n# style 1: sleep_pipe() function creates system cmds\nflowr run x=sleep_pipe platform=local execute=TRUE\n\n# style 2: we start with a tsv of system cmds\n# get example files\nwget --no-check-certificate http://raw.githubusercontent.com/sahilseth/flowr/master/inst/pipelines/sleep_pipe.tsv\nwget --no-check-certificate http://raw.githubusercontent.com/sahilseth/flowr/master/inst/pipelines/sleep_pipe.def\n\n# submit to local machine\nflowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=local execute=TRUE\n# submit to local LSF cluster\nflowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=lsf execute=TRUE\n```\n\n**Example pipelines** [inst/pipelines](https://github.com/flow-r/flowr/tree/master/inst/pipelines)\n\n### Resources\n- For a quick overview, you may browse through,\n these [introductory slides](http://sahilseth.com/slides/flowrintro/).\n- The [overview](http://flow-r.github.io/flowr/overview.html) provides additional details regarding\nthe ideas and concepts used in flowr\n- We have a [tutorial](http://flow-r.github.io/flowr/tutorial.html) which can walk you through creating a\nnew pipeline\n- Additionally, a subset of important functions are described in the [package reference](http://flow-r.github.io/flowr/rd.html)\npage\n- You may follow detailed instructions on [installing and configuring](http://flow-r.github.io/flowr/install.html)\n- You can use flow creator: https://sseth.shinyapps.io/flow_creator), a shiny app to aid in\n\tdesigning a *shiny* new flow. This provides a good example of the concepts\n\n### Updates\nThis package is under active-development, \nyou may watch for changes using\nthe [watch link above](https://help.github.com/articles/watching-repositories/).\n\n### Feedback\nPlease feel free to raise a [github issue](https://github.com/flow-r/flowr/issues) with questions and comments.\n\n### Acknowledgements\n\n-   Jianhua Zhang\n-   Samir Amin\n-   Roger Moye\n-   Kadir Akdemir\n-   Ethan Mao\n-   Henry Song\n-   An excellent resource for writing your own R packages:\n    [r-pkgs.org](https://r-pkgs.org/)\n\n\u003c!--why this license http://kbroman.org/pkg_primer/pages/licenses.html --\u003e\n\u003cscript src = \"vignettes/files/googl.js\"\u003e\u003c/script\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflow-r%2Fflowr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fflow-r%2Fflowr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflow-r%2Fflowr/lists"}