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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, the poseidon server-client infrastructure.

The Minotaur Workflow

Flowchart of the Minotaur Workflow

The Minotaur Workflow consists of three parts:

  • Creating the Poseidon Package recipe
  • Processing of the public data with nf-core/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, 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.

Processing of data with nf-core/eager

This step takes place locally at MPI-EVA. The machinery described in the poseidon-eager GitHub repository 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.