Inconsistent use of vep and vep_file in run_eggla_gwas()

[burrowsk]

Bug description

The parameter to add the path to a VEP annotation file is vep within run_eggla_gwas() [line 95]. the parameter vep is called in line 443 vep_file = vep, however, all other instances specify vep_file which causes the function to exit upon the first instance [lines 408-423]. Only applicable should a user want to specify a vep file.

if (nzchar(system.file(package = "future.apply"))) {
    eggla_lapply <- function(X, basename_file, vep_file, bin_path, bcftools_view_options, build, strand, info_type, FUN) {
      future.apply::future_lapply(
        X = X,
        basename_file = basename_file,
        vep_file = vep_file,
        bin_path = bin_path,
        bcftools_view_options = bcftools_view_options,
        build = build,
        strand = strand,
        info_type = info_type,
        future.globals = FALSE,
        future.packages = "data.table",
        FUN = FUN
      )
    }

eggla version output

eggla 0.18.5

Checklist

• [X] formatted your issue so it is easier for us to read?
• [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• [X] documented the version of eggla you're running, by pasting the output from running packageVersion('eggla') in the "eggla version output" text area?
• [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.

[mcanouil]

This is normal, "vep_file" is internal when defined eggla_lapply. Although I simplified this and anyway renamed the main argument to be more consistent with syntax of other arguments.

I believe the issue you are having is somewhere else, i.e., https://github.com/mcanouil/eggla/blob/1eb2dd56b4c0f883493f99e8d186425361ca4ffd/R/run_eggla_gwas.R#L449-L480

Note that the changes are in the current PR #97