fix: remove regex_moo from params

Author: kelly-sovacool

.codeocean/app-panel.json

@@ -31,16 +31,6 @@
 		}
 	],
 	"parameters": [
-		{
-			"id": "ZvGNzbTfFDAiJ8Lv",
-			"category": "7Rr6IxOMDucKMImp",
-			"name": "multiOmicDataSet file pattern",
-			"param_name": "regex_moo",
-			"description": "Regex pattern used to locate the multiOmicDataSet .rds file",
-			"type": "text",
-			"value_type": "string",
-			"default_value": ".*\\\\.rds$"
-		},
 		{
 			"id": "count_type_id",
 			"category": "FvI4Z2eb9sjL47Jt",

code/main.R

@@ -19,7 +19,6 @@ write_csv(pkg_versions, file.path(results_dir, 'r-packages.csv'))
 # parse CLI arguments
 parser <- ArgumentParser()
 
-parser$add_argument("--regex_moo", type="character", default=".*\\.rds$")
 parser$add_argument("--count_type", type="character", default="filt")
 parser$add_argument("--sub_count_type", type="character", default=NULL, help="Sub count type if count_type is a list")
 parser$add_argument("--feature_id_colname", type="character", default=NULL, help="Column name for feature IDs")
@@ -51,11 +50,12 @@ parse_vector_with_default <- function(x, default) {
 }
 
 # validate inputs
+regex_moo <- ".*\\.rds$"
 data_files <- list.files(file.path('../data'), recursive = TRUE, full.names = TRUE)
-moo_files <- Filter(\(x) str_detect(x, regex(args$regex_moo, ignore_case = TRUE)), data_files)
+moo_files <- Filter(\(x) str_detect(x, regex(regex_moo, ignore_case = TRUE)), data_files)
 
 if (length(moo_files) == 0) {
-    stop(glue("No files matching regex: {args$regex_moo}"))
+    stop(glue("No files matching regex: {regex_moo}"))
 }
 moo_filename <- moo_files[1]
 moo <- read_rds(moo_filename)