{"id":22313936,"url":"https://github.com/ctb/2018-snakemake-cli","last_synced_at":"2025-09-20T03:35:54.008Z","repository":{"id":66659436,"uuid":"125594463","full_name":"ctb/2018-snakemake-cli","owner":"ctb","description":null,"archived":false,"fork":false,"pushed_at":"2019-01-28T19:35:28.000Z","size":2,"stargazers_count":4,"open_issues_count":0,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-29T10:57:31.060Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/ctb.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-03-17T03:47:01.000Z","updated_at":"2020-07-22T21:29:45.000Z","dependencies_parsed_at":"2023-03-27T11:47:33.189Z","dependency_job_id":null,"html_url":"https://github.com/ctb/2018-snakemake-cli","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ctb/2018-snakemake-cli","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2018-snakemake-cli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2018-snakemake-cli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2018-snakemake-cli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2018-snakemake-cli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctb","download_url":"https://codeload.github.com/ctb/2018-snakemake-cli/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2018-snakemake-cli/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":276041592,"owners_count":25574993,"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":"2025-09-20T02:00:10.207Z","response_time":63,"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":[],"created_at":"2024-12-03T22:08:34.062Z","updated_at":"2025-09-20T03:35:54.000Z","avatar_url":"https://github.com/ctb.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 2018-snakemake-cli\n\nAn example of parameterizing snakemake workflows with a simple CLI.\n\nUsage:\n```\n./run \u003cworkflow_file\u003e \u003cparameters_file\u003e\n```\n\ne.g.\n\n```\nrm -f hello.txt\n./run workflow-hello params-amy\n```\ncreates `hello.txt` with \"hello amy\" in it, while\n\n```\nrm -f hello.txt\n./run workflow-hello params-beth\n```\ncreates `hello.txt` with \"hello beth\" in it.\n\nHere, the workflow file `workflow-hello.json` specifes the target\n`hello.txt`, while the parameters file `params-amy` parameterizes\nthe workflow with the name \"amy\".\n\nLikewise,\n\n```\nrm -f goodbye.txt\n./run workflow-goodbye params-beth\n```\n\nwill put `goodbye beth` in `goodbye.txt`.\n\nAll workflows use the same set of Snakemake rules in `Snakefile`.\n\nSee also: https://github.com/charlesreid1/2019-snakemake-cli\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2018-snakemake-cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctb%2F2018-snakemake-cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2018-snakemake-cli/lists"}