Dokumentation

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Generate#

bdp generate reads your bdp.lock and emits ready-to-use configuration files for popular workflow managers and languages. Each target produces format-specific output with resolved cache paths.

Usage#

bash
bdp generate <target>

Targets#

TargetOutputDescription
pythonbdp_data.pypathlib.Path variables per source
snakemakeconfig/bdp_data.yamlYAML config block for configfile:
nextflowconf/bdp_data.configNextflow params.bdp.* block
cwlcwl/bdp-inputs.ymlCWL v1.2 typed File entries with EDAM format annotations
rr/bdp_data.yml + r/bdp_data.RYAML config with Bioconductor reader hints + loader script

Examples#

Python#

bash
bdp generate python

Output (bdp_data.py):

python
"""BDP data paths - auto-generated by 'bdp generate python'. Do not edit."""
from pathlib import Path
_BASE = Path(__file__).parent
# Source: uniprot:P01308-fasta@2024.03
UNIPROT_P01308_FASTA = _BASE / ".bdp" / "data" / "sources" / "uniprot" / "P01308" / "2024.03" / "P01308_2024.03.fasta"
# Source: clinvar:variants-vcf@2024.01
CLINVAR_VARIANTS_VCF = _BASE / ".bdp" / "data" / "sources" / "clinvar" / "variants" / "2024.01" / "variants_2024.01.vcf"

Snakemake#

bash
bdp generate snakemake

Output (config/bdp_data.yaml):

yaml
# BDP data paths - auto-generated by 'bdp generate snakemake'. Do not edit.
# Include in Snakefile: configfile: "config/bdp_data.yaml"
bdp:
clinvar_variants_vcf: ".bdp/data/sources/clinvar/variants/2024.01/variants_2024.01.vcf"
uniprot_p01308_fasta: ".bdp/data/sources/uniprot/P01308/2024.03/P01308_2024.03.fasta"

Nextflow#

bash
bdp generate nextflow

Output (conf/bdp_data.config):

groovy
// BDP data paths - auto-generated by 'bdp generate nextflow'. Do not edit.
// Include in nextflow.config: includeConfig 'conf/bdp_data.config'
params {
bdp {
clinvar_variants_vcf = "${projectDir}/.bdp/data/sources/clinvar/variants/2024.01/variants_2024.01.vcf"
uniprot_p01308_fasta = "${projectDir}/.bdp/data/sources/uniprot/P01308/2024.03/P01308_2024.03.fasta"
}
}

CWL#

bash
bdp generate cwl

Output (cwl/bdp-inputs.yml):

yaml
# BDP data inputs - auto-generated by 'bdp generate cwl'. Do not edit.
# Usage: cwltool my-workflow.cwl cwl/bdp-inputs.yml
# CWL v1.2 - https://www.commonwl.org/v1.2/
clinvar_variants_vcf:
class: File
format: edam:format_3016
path: ../.bdp/data/sources/clinvar/variants/2024.01/variants_2024.01.vcf
uniprot_p01308_fasta:
class: File
format: edam:format_1929
path: ../.bdp/data/sources/uniprot/P01308/2024.03/P01308_2024.03.fasta

R#

bash
bdp generate r

Output (r/bdp_data.yml):

yaml
# BDP data paths - auto-generated by 'bdp generate r'. Do not edit.
sources:
clinvar_variants_vcf:
path: "../.bdp/data/sources/clinvar/variants/2024.01/variants_2024.01.vcf"
format: vcf
reader: "VariantAnnotation::readVcf"
package: "VariantAnnotation"
packages:
bioconductor:
- VariantAnnotation
cran:
- yaml

Plus r/bdp_data.R — a loader script with bdp_install_packages() helper.

Notes#

  • Paths reflect the local cache — run bdp pull first to ensure files are present
  • Re-run after bdp pull if versions change
  • CWL and R generators are format-aware: EDAM URIs and Bioconductor package hints are derived from the source format
  • See Integrations for tool-specific usage guides and full bioinformatics examples