tests/testthat/test_cutadapt.R

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

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_equal(length(res_cut), 1)
    expect_type(res_cut[[1]], "character")

    expect_equal(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_equal(length(res_cut2), 2)

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

    expect_equal(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_equal(length(res_cut3), 2)
    expect_type(res_cut3[[1]], "character")

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

  unlink(tempdir(), recursive = TRUE)
}