Configuration
The main runtime configuration lives in YAML files.
Common files include:
bin/config.yaml: default local runtime configurationbin/cnag-hpc-config.yaml: CNAG HPC-oriented configurationtestdata/vcf/param.yaml: VCF test configurationtestdata/tsv/param.yaml: SNP-array TSV test configurationexamples/param_hg38.yaml: GRCh38 / hg38 example configuration
Common Parameters
| Parameter | Purpose |
|---|---|
genome | Reference genome label, such as hg19, hg38, hs37, or b37 |
projectdir | Output project directory |
bff2html | Whether to generate browser-oriented HTML output |
annotate | Whether the VCF workflow should run annotation |
bff.metadatadir | Directory containing metadata BFF JSON collections for loading |
bff.genomicVariationsVcf | Path to generated genomic variation output |
Keep the genome setting aligned with the VCF contig naming and annotation resources used by your installation.