tests/testthat/test-moduleMessages.R

In ngsReports: Load FastqQC reports and other NGS related files

context("Test that messages appear when modules are missing from some files")

f <- c(
    system.file("extdata/ATTG_R1_fastqc.zip", package = "ngsReports"),
    system.file(
        "extdata/errorTestingFiles/moduleNamesNoData.zip",
        package = "ngsReports"
    )
)
fdl <- FastqcDataList(f)

test_that("All modules give correct messages",{
  expect_message(getModule(fdl, "Adapter_Content"))
  expect_message(getModule(fdl, "Basic_Statistics"))
  expect_message(getModule(fdl, "Kmer_Content"))
  expect_message(getModule(fdl, "Overrepresented_sequences"))
  expect_message(getModule(fdl, "Per_base_N_content"))
  expect_message(getModule(fdl, "Per_base_sequence_content"))
  expect_message(getModule(fdl, "Per_base_sequence_quality"))
  expect_message(getModule(fdl, "Per_sequence_GC_content"))
  expect_message(getModule(fdl, "Per_sequence_quality_scores"))
  expect_message(getModule(fdl, "Per_tile_sequence_quality"))
  expect_message(getModule(fdl, "Sequence_Duplication_Levels"))
  expect_message(getModule(fdl, "Sequence_Length_Distribution"))
  expect_message(getModule(fdl, "Total_Deduplicated_Percentage"))
})

closeAllConnections()