Update function to get example to produce output

grunwaldlab · Jul 26, 2024 · 42935b4 · 42935b4
1 parent d7ad3ba
commit 42935b4
Show file tree

Hide file tree

Showing 8 changed files with 8 additions and 8 deletions.
diff --git a/R/assign_taxonomy.R b/R/assign_taxonomy.R
@@ -277,7 +277,7 @@ process_single_barcode <-
 #' analysis_setup<-prepare_reads(
 #'   data_directory = system.file("extdata", package = "demulticoder"), 
 #'   output_directory = "~/package_output",
-#'   tempdir_path = tempdir(),
+#'   tempdir_path = "~/temp",
 #'   tempdir_id = "demulticoder_run_temp", 
 #'   overwrite_existing = FALSE
 #' )

diff --git a/R/convert_asv_matrix.R b/R/convert_asv_matrix.R
@@ -22,7 +22,7 @@
 #' analysis_setup<-prepare_reads(
 #'   data_directory = system.file("extdata", package = "demulticoder"), 
 #'   output_directory = "~/package_output",
-#'   tempdir_path = tempdir(),
+#'   tempdir_path = "~/temp",
 #'   tempdir_id = "demulticoder_run_temp", 
 #'   overwrite_existing = FALSE
 #' )

diff --git a/R/cut_primers_trim_reads.R b/R/cut_primers_trim_reads.R
@@ -290,7 +290,7 @@ plot_post_trim_qc <- function(cutadapt_data, output_directory_path, n = 500000)
 #' analysis_setup<-prepare_reads(
 #'   data_directory = system.file("extdata", package = "demulticoder"), 
 #'   output_directory = "~/package_output",
-#'   tempdir_path = tempdir(),
+#'   tempdir_path = "~/temp",
 #'   tempdir_id = "demulticoder_run_temp", 
 #'   overwrite_existing = FALSE
 #' )

diff --git a/R/prepare_reads_count_primers.R b/R/prepare_reads_count_primers.R
@@ -471,7 +471,7 @@ make_cutadapt_tibble <-
 #' analysis_setup<-prepare_reads(
 #'   data_directory = system.file("extdata", package = "demulticoder"), 
 #'   output_directory = "~/package_output",
-#'   tempdir_path = tempdir(),
+#'   tempdir_path = "~/temp",
 #'   tempdir_id = "demulticoder_run_temp", 
 #'   overwrite_existing = FALSE
 #' )

diff --git a/man/assign_tax.Rd b/man/assign_tax.Rd
diff --git a/man/convert_asv_matrix_to_objs.Rd b/man/convert_asv_matrix_to_objs.Rd
diff --git a/man/cut_trim.Rd b/man/cut_trim.Rd
diff --git a/man/prepare_reads.Rd b/man/prepare_reads.Rd