R script template using optparse

rscript_template.R

#!/usr/bin/env Rscript

###############################################################################

# Package names for non-test dependencies
pkgs <- c(
  # CRAN
  "magrittr",
  "optparse",
  # Bioconductor
  # Local
  NULL
)

for (pkg in pkgs) {
  suppressPackageStartupMessages(
    library(pkg, character.only = TRUE)
  )
}

###############################################################################

define_parser <- function() {
  description <- paste(
    "Run my awesome workflow on some data."
  )

  parser <- OptionParser(
    description = description
  ) %>%
    add_option(
      c("--input", "-i"), type = "character",
      help = paste(
        "Some filename."
      )
    ) %>%
    add_option(
      "--threshold", type = "double",
      help = paste(
        "A numeric option."
      )
    ) %>%
    add_option(
      "--filter_flag", action = "store_true", default = FALSE,
      help = paste(
        "Should the filter-flag be applied? Default: FALSE (no filters)"
      )
    ) %>%
    add_option(
      c("--output", "-o"), type = "character", default = "output.tsv",
      help = paste(
        "Another filename, but with a default value."
      )
    ) %>%
    add_option(
      "--test", action = "store_true", default = FALSE,
      help = "Run any script-embedded tests then exit."
    )
}

###############################################################################

run_my_awesome_workflow <- function(x) {
  # Standard convoluted analysis scheme:
  x
}

###############################################################################

{--script_name--} <- function(
    input_file, threshold, filter_flag, output_file
) {
  # Input
  some_data <- scan(input_file, what = "character")

  # Validate the input
  stopifnot(...blah...(some_data))

  # Small number of high-level function calls
  my_results <- run_my_awesome_workflow(some_data)

  # Output
  write(my_results, output_file)
}

###############################################################################

main <- function(opt) {
  # `main` should only parse the command line arguments (eg, split a
  # `--drop_groups A,C` comma-separated string of values; extract some
  # config values from a file), then call the `script_name` function
  {--script_name--}(
    input_file = opt[["input"]],
    threshold = opt[["threshold"]],
    filter_flag = opt[["filter_flag"]],
    output_file = opt[["output"]]
  )
}

###############################################################################

test <- function() {
  # You can add some tests within the script if you want
  stopifnot(requireNamespace("testthat"))

  testthat::expect_equal(run_my_awesome_workflow(1), 1)

  # remove me
  testthat::expect_equal(
    1, 2, info = "a failing test to test the tests that test your code"
  )
}

###############################################################################

opt <- optparse::parse_args(define_parser())

# User can either run the tests or the main function
if (opt[["test"]]) {
  test()
} else {
  main(opt)
}

###############################################################################

#!/usr/bin/env bash                                                                                                               
                                                                                                                                  
# download the master version of the rscript template                                                                             
curl \                                                                                                                            
  https://gist.githubusercontent.com/russHyde/9d91fcb213973b0ace5424b0520c82b7/raw/rscript_template.R

Put the bash script into

<somewhere_on_PATH>/rscript_template

and chmod u+x it. Then use

rscript_template > my_new_script.R