Better bug info

adrientaudiere · Dec 19, 2024 · 7f066cd · 7f066cd
1 parent d2242d7
commit 7f066cd
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/R/dada_phyloseq.R b/R/dada_phyloseq.R
@@ -2484,7 +2484,9 @@ physeq_or_string_to_dna <- function(physeq = NULL, dna_seq = NULL) {
 #'
 #' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' \dontrun{
-#' cutadapt_remove_primers("inst/extdata", "TTC", "GAA",
+#' cutadapt_remove_primers(system.file("extdata", package="MiscMetabar"), 
+#'   "TTC", 
+#'   "GAA",
 #'   folder_output = tempdir()
 #' )
 #'

diff --git a/R/targets_misc.R b/R/targets_misc.R
@@ -33,7 +33,14 @@ list_fastq_files <-
            pattern_R1 = "_R1_",
            pattern_R2 = "_R2_",
            nb_files = Inf) {
+
+    if(length(list.files(path))==0) {
+      stop("There is no files in the folder ", path)
+    }
     list_files <- list.files(path, pattern = pattern, full.names = TRUE)
+    if(length(list_files)==0) {
+      stop("None file in the folder ", path, " match the pattern ", pattern)
+    }
     if (paired_end) {
       fnfs <- sort(list_files[grepl(list_files, pattern = pattern_R1)])
       fnrs <-