update filterBed process

TARGENE / targene-pipeline

Nextflow pipeline for Targeted-Learning of genetic effects

MIT License

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Closed roskamsh closed 1 year ago

roskamsh commented 1 year ago

make compatible with non-UKBB cohorts
objectives include:
1. QC file as an optional argument
2. update generateIIDGenotypes workflow (and consequently IIDGenotypes which contains filterBed)
3. update TarGeneCore.jl/bin/prepare_confounders.jl and TarGeneCore.jl/src/confounders.jl and call these functions correctly from the targene-pipeline process filterBed

roskamsh commented 1 year ago

Completed here: 3f2fcb2e1a35b492840a74ab902c7858f4725f95

And in TargeneCore.jl: 5d00851c0d9eb143ce9b868904a1f8fb2a60a8a8 b728f3cb18d256e211aa5ac069cb40797842b6af e87133b732cb8f5af42fed599c9bbdc63aa420d3

also added new test function for this: 0df054835105df8bdd614e85a57296fede9dba6f 1269eee8fceb786d0f657e94f8026289693b0904