"sankey_pq works with GlobalPatterns dataset"
"sankey_pq works with data_fungi_mini dataset"
"venn_pq works with data_fungi_mini dataset"
"ggvenn_pq works with data_fungi_mini dataset"
"upset_pq works with data_fungi dataset"
"upset_test_pq works with data_fungi_mini dataset"
"plot_LCBD_pq works with data_fungi dataset"
"LCBD_pq works with data_fungi_mini dataset"
"plot_LCBD_pq works with data_fungi_mini dataset"
"plot_SCBD_pq works with data_fungi_mini dataset"
"multipatt_pq works with data_fungi_mini dataset"

multipatt_pq works with data_fungi_mini dataset

Error in `system(paste0("zcat ", file_path, " | grep -ce '^+$'"), intern = TRUE)`: 'zcat' not found

test_that("asv2otu works fine with Clusterize method", {
suppressWarnings(vsearch_error_or_not <- try(system("vsearch 2>&1", intern = TRUE), silent = TRUE))
if (class(vsearch_error_or_not) == "try-error") {
message("lulu_pq() can't be tested when vsearch is not installed")
expect_s4_class(lulu_pq(data_fungi_sp_known, clean_pq = TRUE, verbose = TRUE)$new_physeq, "phyloseq")
suppressWarnings(mumu_error_or_not <- try(system("mumu --help", intern = TRUE), silent = TRUE))
if (class(mumu_error_or_not) == "try-error") {
message("mumu_pq() can't be tested when mumu is not installed")
expect_s4_class(mumu_pq(data_fungi_mini, clean_pq = TRUE, verbose = TRUE)$new_physeq, "phyloseq")
expect_error(verify_pq(df), "The physeq argument is not a valid phyloseq object.")
data_fungi_with__P@tax_table[, "Phylum"] <- paste0("P__", data_fungi_with__P@tax_table[, "Phylum"])
expect_equal(sum(data_fungi_with__P@tax_table[, "Phylum"] == data_fungi_mini@tax_table[, "Phylum"]), 0)
expect_equal(perc(20, 200, add_symbol = TRUE), "10%")
expect_equal(perc(0.1, add_symbol = TRUE), "10%")
expect_error(count_seq("tests/testthat.R"), "The file extension R is not supported.")
# test_that("add_new_taxonomy_pq works fine", {

"asv2otu works fine with Clusterize method"
"lulu_pq() can't be tested when vsearch is not installed"
"mumu_pq() can't be tested when mumu is not installed"
"The physeq argument is not a valid phyloseq object."
"The file extension R is not supported."