tar_vep.R

### global libraries ===============================================================================
library(targets)
library(tarchetypes)
library(here)
library(data.table)
library(future)
library(future.callr)

# targets::tar_renv(extras = "visNetwork", path = "scripts/_dependencies.R")


### project setup ==================================================================================
# Functions/scripts required: tar-vep.R
invisible(sapply(
  X = list.files(here("scripts", "tar-utils"), pattern = "^tar-.*R$", full.names = TRUE),
  FUN = source, echo = FALSE
))

plan(future.callr::callr, workers = 3)
# plan(multicore, workers = 40)
message(sprintf("Number of workers: %d", future::nbrOfWorkers()))
# setDTthreads(threads = 1)


### targets setup ==================================================================================
tar_setup <- list( # Setup project
  tar_target(project, sub("(.*)_[^_]*\\.Rproj$", "\\1", list.files(here(), pattern = ".Rproj$")), packages = "here"),
  tar_target(author, "Mickaël CANOUIL, *Ph.D.*"),
  tar_target(output_directory, here::here("outputs"), packages = "here"),
  tar_target(genome_assembly, "GRCh38"),
  tar_target(ensembl_version, "104"),
  tar_target(ensembl_species, "homo_sapiens"),
  tar_target(vep_cache,
    command = c(
      "server" = "/media/Data/ExternalData/vep_data",
      "docker" = "/disks/DATA/ExternalData/vep_data"
    )
  ),
  tar_target(bcftools, "/usr/bin/bcftools", format = "file"),
  tar_target(tabix, "/usr/bin/tabix", format = "file"),
  tar_target(bgzip, "/usr/bin/bgzip", format = "file")
)


### targets ========================================================================================
tar_vep <- list(
  tar_target(vep_symbol,
    command = get_symbol_vep(
      input = get_variants(
        path = "file.vcf.gz",
        output_directory = output_directory,
        bin_path = list(bcftools = bcftools)
      ),
      output_directory = output_directory,
      genome_assembly = genome_assembly,
      ensembl_version = ensembl_version,
      ensembl_species = ensembl_species,
      vep_cache = vep_cache
    ),
    packages = c("here", "data.table")
  ),
  tar_target(veb_symbol_file,
    command = format_symbol_vep(
      file = vep_symbol,
      bin_path = list(tabix = tabix, bgzip = bgzip)
    ),
    format = "file"
  )
)

list(
  tar_setup,
  tar_vep
)