feat: add BCF input format support#486
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plink2 natively supports BCF via --bcf flag. This adds BCF as a valid input format in the samplesheet, reusing the existing VCF pipeline path with the appropriate plink2 flag.
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Tested successfully on a 1000 Genomes BCF sample: pipeline ran end-to-end without issues. |
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Summary
Closes #483
Adds BCF (Binary VCF) as a supported input format. plink2 natively supports BCF via
--bcf, so this reuses the existing VCF pipeline path with minimal changes.Changes
bcfas a valid value in the samplesheetformatcolumn--bcfinstead of--vcfinPLINK2_VCFwhen input is BCF.csiindex inSamplesheetParsertest_bcf), and test moduleTest plan
nextflow run main.nf -profile test_bcf,dockerpasses