Dokumentation

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Tools & Bundles#

Beyond raw data files, BDP can manage tool bundles — versioned collections that combine a dataset with processing scripts, schema definitions, or post-pull hooks.

What Is a Tool Bundle?#

A tool bundle is a source entry in bdp.yml that may include:

  • One or more data files
  • A hooks.post_pull script to transform or index the data after download
  • Metadata for citation generation
  • A pinned version in bdp.lock

Defining a Tool Bundle#

In bdp.yml:

yaml
sources:
- uniprot:swissprot-fasta@1.0

Workflow Integration#

Tool bundles integrate natively with workflow managers:

bash
# Generate a Snakemake input block
bdp generate snakemake
# Generate a Nextflow params block
bdp generate nextflow
# Generate a Python paths dict
bdp generate python

These commands read bdp.lock and emit ready-to-use configuration for your pipeline.

Relationship to Data Sources#

| Concept | Description | |---|---| | Data source | A single versioned file from an organization | | Bundle | A pre-assembled collection of related data sources | | Tool bundle | A source + optional hooks + workflow metadata | | Project | A collection of sources managed via bdp.yml |