Run msconvert in parallel from R

parallel_msconvert.R

# Requires IDBac function findMSconvert()
parallel_msconvert <- function(directory){

  # File paths
  raw_path <- file.path(directory)
  raw_files <- list.files(raw_path,
                          full.names = TRUE)
  mzml_dir <- file.path(dirname(raw_path),
                        "mzml")
  dir.create(mzml_dir)


  # Run msconvert in parallel
  msconvert_location <- normalizePath(IDBacApp::findMSconvert(),
                                      winslash = "/")


  msconvert_cmd <- lapply(raw_files,
                          function(raw_files){
                            paste0(shQuote(msconvert_location),
                                   " ",
                                   shQuote(raw_files),
                                   " ",
                                   "--mzML",
                                   " ",
                                   '--filter "peakPicking true 1-" --filter "threshold count 100 most-intense"',
                                   " ",
                                   "-o",
                                   " ",
                                   shQuote(mzml_dir))
                          })



  numCores <- parallel::detectCores()
  numCores <- ifelse(numCores > 2,
                     numCores - 1,
                     1)
  cl <- parallel::makeCluster(numCores)

  functionTOrunMSCONVERTonCMDline <- function(x){
    system(command = x,
           invisible = T,
           wait = TRUE)
  }

  parallel::parLapply(cl,
                      msconvert_cmd,
                      functionTOrunMSCONVERTonCMDline)
  parallel::stopCluster(cl)

}