https://github.com/poseidon-framework/minotaur-recipes
Package recipes for processing through the Minotaur workflow
https://github.com/poseidon-framework/minotaur-recipes
Last synced: 1 day ago
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Package recipes for processing through the Minotaur workflow
- Host: GitHub
- URL: https://github.com/poseidon-framework/minotaur-recipes
- Owner: poseidon-framework
- License: gpl-3.0
- Created: 2023-08-28T12:54:39.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2026-03-23T16:53:46.000Z (14 days ago)
- Last Synced: 2026-03-24T14:09:12.409Z (13 days ago)
- Language: Shell
- Size: 1.24 MB
- Stars: 2
- Watchers: 2
- Forks: 16
- Open Issues: 103
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# minotaur-recipes
This repository holds all the recipes used to run the Poseidon Framework's
**Minotaur Workflow** and create poseidon packages.
The Minotaur workflow takes in sequencing metadata and URLs of publicly archived
raw sequencing data (provided by the community) and processes them in a flexibly
configurable yet reproducible manner to produce poseidon packages. These
poseidon packages are then added to the Poseidon Minotaur Archive (PMA), and
made available to everyone through
[`trident`](https://github.com/poseidon-framework/poseidon-hs), the poseidon
server-client infrastructure.
# The Minotaur Workflow
The Minotaur Workflow consists of three parts:
- Creating the Poseidon Package recipe
- Processing of the public data with [nf-core/eager](https://nf-co.re/eager)
- Poseidon Package preparation for upload to the PMA
Details on each part can be found below.
## Creating a Poseidon Package recipe
This is the community-facing entrypoint to the workflow, and takes place on the
[minotaur-recipes GitHub repository](https://github.com/poseidon-framework/minotaur-recipes),
when a contributor has opened a pull request to add/update a package. Once the
required SSF file has been updated, `delphis-bot` will create all the
SSF-associated auxilliary files required for processing.
Upon activation, `delphis-bot` will create:
- a precursor nf-core/eager TSV input file,
- the package `.config` file,
- the package `tsv_patch.sh` that can be ued to localise the TSV precursor into
a valid input for nf-core/eager,
- a `script_versions.txt` file, with the versions of the scripts used during the
package recipe creation.
For a step-by-step guide on how to contribute to the PMA, see
[this guide](https://www.poseidon-adna.org/#/minotaur?id=requesting-a-package-recipe).
## Processing of data with nf-core/eager
This step takes place locally at [MPI-EVA](https://www.eva.mpg.de/index). The
machinery described in the
[poseidon-eager GitHub repository](https://github.com/poseidon-framework/poseidon-eager)
uses the package recipe to:
- download the raw data from the public archive URLs in the SSF file (using
`scripts/download_ena_data.py` and `scripts/run_download.sh`)
- Validate the downloaded data, and create symlinks with clearer naming
(`scripts/validate_downloaded_data.sh`). This allows the one-to-many
relationship between raw data and `poseidon_ids`.
- Apply the `*_tsv_patch.sh` of the package recipe to create the finalised
nf-core/eager TSV.
- Use `run_eager.sh` to run nf-core/eager.
- This uses the finalised TSV as its input
- And load the `.config` of the package recipe to apply all default
parameters, as well as any relevant `CaptureType` and package-specific
parameters.
Once the data is processed, the genotyping output of nf-core/eager is used to
create a poseidon package. The metadata included in the janno file for this
package is then filled using descriptive statistics generated by nf-core/eager
and information from the SSF file.