tests/testthat/test_cutadapt.R

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

if (FALSE) {
  # Not running test for the moment because can't fix for test-coverage.yaml github action
  if (!MiscMetabar:::is_cutadapt_installed()) {
    message(
      "cutadapt_remove_primers()  can't be
    tested when cutadapt is not installed"
    )
  } else if (FALSE) {
    # Not running test for the moment because can't fix for test-coverage.yaml github action
    test_that("cutadapt_remove_primers works fine", {
      skip_on_cran()
      skip_on_os("windows")
      expect_silent(suppressMessages(
        res_cut <- cutadapt_remove_primers(
          "inst/extdata",
          "TTC",
          "GAA",
          folder_output = paste0(tempdir(), "/output_cutadapt")
        )
      ))
      expect_type(res_cut, "list")
      expect_length(res_cut, 1)
      expect_type(res_cut[[1]], "character")

      expect_length(
        list.files(
          paste0(tempdir(), "/output_cutadapt")
        ),
        2
      )

      expect_silent(suppressMessages(
        res_cut2 <- cutadapt_remove_primers(
          system.file("extdata", package = "dada2"),
          pattern_R1 = "F.fastq.gz",
          pattern_R2 = "R.fastq.gz",
          primer_fw = "TTC",
          primer_rev = "GAA",
          folder_output = tempdir()
        )
      ))

      expect_type(res_cut2, "list")
      expect_length(res_cut2, 2)

      expect_type(res_cut2[[1]], "character")

      expect_length(
        list.files(
          paste0(tempdir(), "/output_cutadapt")
        ),
        2
      )

      expect_silent(suppressMessages(
        res_cut3 <- cutadapt_remove_primers(
          system.file("extdata", package = "dada2"),
          pattern_R1 = "F.fastq.gz",
          primer_fw = "TTC",
          folder_output = tempdir(),
          cmd_is_run = FALSE
        )
      ))

      expect_type(res_cut3, "list")
      expect_length(res_cut3, 2)
      expect_type(res_cut3[[1]], "character")

      expect_length(
        list.files(
          paste0(tempdir(), "/output_cutadapt")
        ),
        2
      )
    })

    unlink(tempdir(), recursive = TRUE)
  }
}