{"id":48054993,"url":"https://github.com/poseidon-framework/minotaur-recipes","last_synced_at":"2026-04-04T14:25:41.620Z","repository":{"id":193506079,"uuid":"684095558","full_name":"poseidon-framework/minotaur-recipes","owner":"poseidon-framework","description":"Package recipes for processing through the Minotaur workflow","archived":false,"fork":false,"pushed_at":"2026-03-23T16:53:46.000Z","size":1295,"stargazers_count":2,"open_issues_count":103,"forks_count":16,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-03-24T14:09:12.409Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/poseidon-framework.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,"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":"2023-08-28T12:54:39.000Z","updated_at":"2026-03-23T16:53:59.000Z","dependencies_parsed_at":"2024-03-26T13:46:44.432Z","dependency_job_id":"5b9a59bc-c9e7-4579-a2a6-be8550695a0b","html_url":"https://github.com/poseidon-framework/minotaur-recipes","commit_stats":null,"previous_names":["poseidon-framework/minotaur-recipes"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/poseidon-framework/minotaur-recipes","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/poseidon-framework%2Fminotaur-recipes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/poseidon-framework%2Fminotaur-recipes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/poseidon-framework%2Fminotaur-recipes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/poseidon-framework%2Fminotaur-recipes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/poseidon-framework","download_url":"https://codeload.github.com/poseidon-framework/minotaur-recipes/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/poseidon-framework%2Fminotaur-recipes/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31402414,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-04T10:20:44.708Z","status":"ssl_error","status_checked_at":"2026-04-04T10:20:06.846Z","response_time":60,"last_error":"SSL_read: 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":"2026-04-04T14:25:36.379Z","updated_at":"2026-04-04T14:25:41.606Z","avatar_url":"https://github.com/poseidon-framework.png","language":"Shell","readme":"# minotaur-recipes\n\n![](docs/images/Poseidon-Logo-WaterGraphicLrg.png)\n\nThis repository holds all the recipes used to run the Poseidon Framework's\n**Minotaur Workflow** and create poseidon packages.\n\nThe Minotaur workflow takes in sequencing metadata and URLs of publicly archived\nraw sequencing data (provided by the community) and processes them in a flexibly\nconfigurable yet reproducible manner to produce poseidon packages. These\nposeidon packages are then added to the Poseidon Minotaur Archive (PMA), and\nmade available to everyone through\n[`trident`](https://github.com/poseidon-framework/poseidon-hs), the poseidon\nserver-client infrastructure.\n\n# The Minotaur Workflow\n\n![Flowchart of the Minotaur Workflow](docs/images/Minotaur_Workflow.jpg)\n\nThe Minotaur Workflow consists of three parts:\n\n- Creating the Poseidon Package recipe\n- Processing of the public data with [nf-core/eager](https://nf-co.re/eager)\n- Poseidon Package preparation for upload to the PMA\n\nDetails on each part can be found below.\n\n## Creating a Poseidon Package recipe\n\nThis is the community-facing entrypoint to the workflow, and takes place on the\n[minotaur-recipes GitHub repository](https://github.com/poseidon-framework/minotaur-recipes),\nwhen a contributor has opened a pull request to add/update a package. Once the\nrequired SSF file has been updated, `delphis-bot` will create all the\nSSF-associated auxilliary files required for processing.\n\nUpon activation, `delphis-bot` will create:\n\n- a precursor nf-core/eager TSV input file,\n- the package `.config` file,\n- the package `tsv_patch.sh` that can be ued to localise the TSV precursor into\n  a valid input for nf-core/eager,\n- a `script_versions.txt` file, with the versions of the scripts used during the\n  package recipe creation.\n\nFor a step-by-step guide on how to contribute to the PMA, see\n[this guide](https://www.poseidon-adna.org/#/minotaur?id=requesting-a-package-recipe).\n\n## Processing of data with nf-core/eager\n\nThis step takes place locally at [MPI-EVA](https://www.eva.mpg.de/index). The\nmachinery described in the\n[poseidon-eager GitHub repository](https://github.com/poseidon-framework/poseidon-eager)\nuses the package recipe to:\n\n- download the raw data from the public archive URLs in the SSF file (using\n  `scripts/download_ena_data.py` and `scripts/run_download.sh`)\n- Validate the downloaded data, and create symlinks with clearer naming\n  (`scripts/validate_downloaded_data.sh`). This allows the one-to-many\n  relationship between raw data and `poseidon_ids`.\n- Apply the `*_tsv_patch.sh` of the package recipe to create the finalised\n  nf-core/eager TSV.\n- Use `run_eager.sh` to run nf-core/eager.\n  - This uses the finalised TSV as its input\n  - And load the `.config` of the package recipe to apply all default\n    parameters, as well as any relevant `CaptureType` and package-specific\n    parameters.\n\nOnce the data is processed, the genotyping output of nf-core/eager is used to\ncreate a poseidon package. The metadata included in the janno file for this\npackage is then filled using descriptive statistics generated by nf-core/eager\nand information from the SSF file.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fposeidon-framework%2Fminotaur-recipes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fposeidon-framework%2Fminotaur-recipes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fposeidon-framework%2Fminotaur-recipes/lists"}