Integrations#

BDP integrates with the major bioinformatics workflow managers and languages. Once you have a bdp.yml and a populated bdp.lock, use bdp generate to emit a configuration file for your tool — resolved file paths, pinned to exact versions.

Supported Integrations#

Integration	Command	Output
Python	`bdp generate python`	`bdp_data.py` — `pathlib.Path` variables per source
Snakemake	`bdp generate snakemake`	`config/bdp_data.yaml` — YAML config block
Nextflow	`bdp generate nextflow`	`conf/bdp_data.config` — `params.bdp.*` block
CWL	`bdp generate cwl`	`cwl/bdp-inputs.yml` — CWL v1.2 typed File entries with EDAM format annotations
R	`bdp generate r`	`r/bdp_data.yml` + `r/bdp_data.R` — YAML config with Bioconductor reader hints

Typical Workflow#

bash

# 1. Add data sources
bdp source add uniprot:P01308-fasta@2024.03
bdp source add clinvar:variants-vcf@2024.01
bdp source add ensembl:homo_sapiens-gtf@110
 
# 2. Pull data
bdp pull
 
# 3. Generate integration config for your tool
bdp generate cwl    # or python, snakemake, nextflow, r
 
# 4. Use the generated config in your pipeline
cwltool variant-analysis.cwl cwl/bdp-inputs.yml

The generated files always reflect the current bdp.lock — re-run after any bdp pull that changes versions, or automate it with a post-pull hook.

Format-Aware Generation#

BDP knows the file format of each source (FASTA, VCF, GTF, OBO, TSV, etc.) and uses this to generate richer output:

CWL: EDAM ontology format annotations (edam:format_1929 for FASTA, edam:format_3016 for VCF, etc.)
R: Recommended Bioconductor reader function and package for each format (e.g., Biostrings::readAAStringSet for FASTA, VariantAnnotation::readVcf for VCF)

Post-Pull Hooks#

Automate code generation so your integration config stays in sync:

yaml

# bdp.yml
hooks:
  post_pull:
    - bdp generate cwl
    - bdp generate r

See Post-Pull Hooks for the full hook API.

Examples#