{"id":32216376,"url":"https://github.com/biosails/biox-workflow-command","last_synced_at":"2025-10-22T07:58:34.039Z","repository":{"id":56829917,"uuid":"78095399","full_name":"biosails/BioX-Workflow-Command","owner":"biosails","description":null,"archived":false,"fork":false,"pushed_at":"2018-07-02T17:06:14.000Z","size":304,"stargazers_count":0,"open_issues_count":11,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2023-10-29T11:28:49.509Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","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/biosails.png","metadata":{"files":{"readme":"README.md","changelog":"Changes","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-01-05T08:40:34.000Z","updated_at":"2018-06-06T11:45:08.000Z","dependencies_parsed_at":"2022-09-02T04:00:40.485Z","dependency_job_id":null,"html_url":"https://github.com/biosails/BioX-Workflow-Command","commit_stats":null,"previous_names":[],"tags_count":31,"template":null,"template_full_name":null,"purl":"pkg:github/biosails/BioX-Workflow-Command","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosails%2FBioX-Workflow-Command","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosails%2FBioX-Workflow-Command/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosails%2FBioX-Workflow-Command/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosails%2FBioX-Workflow-Command/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosails","download_url":"https://codeload.github.com/biosails/BioX-Workflow-Command/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosails%2FBioX-Workflow-Command/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280402186,"owners_count":26324587,"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":"2025-10-22T02:00:06.515Z","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":"2025-10-22T07:58:31.077Z","updated_at":"2025-10-22T07:58:34.034Z","avatar_url":"https://github.com/biosails.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NAME\n\nBioX::Workflow::Command - Opinionated Bioinformatics Genomics Workflow Creator\n\n# SYNOPSIS\n\n    biox run -w workflow.yml\n    biox -h\n\n# documentation\n\nFull documentation is available at gitbooks. [Documentation ](https://metacpan.org/pod/\nhttps:#biosails.gitbooks.io-biox-workflow-command-docs-content)\n\n# Quick Start\n\n## Get Help\n\n    #Global Help\n    biox --help\n    biox-workflow.pl --help\n    #Help Per Command\n    biox run --help\n\n## Run a Workflow\n\n    #Previously biox-workflow.pl --workflow workflow.yaml\n    biox run -w workflow.yml #or --workflow\n    biox-workflow.pl run --workflow workflow.yml\n\n## Run a Workflow with make like utilities\n\nUsing the option --auto\\_deps will create #HPC deps based on your INPUT/OUTPUTs -\nuse this with caution. It will only work correctly if INPUT/OUTPUT is complete\nand accurate.\n\n    biox run --workflow workflow.yml --auto_deps\n\n## Create a new workflow\n\nThis creates a new workflow with rules rule1, rule2, rule3, with a few variables\nto help get you started.\n\n    biox new -w workflow.yml --rules rule1,rule2,rule3\n\n## Add a new rule to a workflow\n\nAdd new rules to an existing workflow.\n\n    biox add -w workflow.yml --rules rule4\n\n## Check the status of files in your workflow\n\nYou must have defined INPUT/OUTPUTs to make use of this rule. If you do, biox\nwill output a table with information about your files.\n\n    biox stats -w workflow.yml\n\n# DESCRIPTION\n\nBioX::Workflow::Command is a templating system for creating Bioinformatics Workflows.\n\n# AUTHOR\n\nJillian Rowe \u003cjillian.e.rowe@gmail.com\u003e\n\n# COPYRIGHT\n\nCopyright 2017- Jillian Rowe\n\n# LICENSE\n\nThis library is free software; you can redistribute it and/or modify\nit under the same terms as Perl itself.\n\n# Acknowledgements\n\nAs of version 0.03:\n\nThis modules continuing development is supported\nby NYU Abu Dhabi in the Center for Genomics and\nSystems Biology. With approval from NYUAD, this\ninformation was generalized and put on github,\nfor which the authors would like to express their\ngratitude.\n\nBefore version 0.03\n\nThis module was originally developed at and for Weill Cornell Medical\nCollege in Qatar within ITS Advanced Computing Team. With approval from\nWCMC-Q, this information was generalized and put on github, for which\nthe authors would like to express their gratitude.\n\n# SEE ALSO\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosails%2Fbiox-workflow-command","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosails%2Fbiox-workflow-command","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosails%2Fbiox-workflow-command/lists"}