From c0689fac784acc0d1a342f0566ec701da0212646 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 7 May 2024 17:04:58 -0400
Subject: [PATCH] bug fix for issue #28: sort and not recurse image_directory

---
 subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
index 21cd0e1..c061f25 100644
--- a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
@@ -325,11 +325,10 @@ def make_ashlar_input_sample( samplesheet_row ) {
     } else {
         // TODO: remove this option or allow it to grab all files when no column in the samplesheet?
         def image_dir = samplesheet_row[index_sample_image_directory]
-        image_dir.eachFileRecurse (FileType.FILES) {
-            if(it.toString().endsWith(".ome.tif")){
-                cycle_images << file(it)
-            }
+        image_dir.eachFileMatch (FileType.FILES, ~/^.*\.ome.tif$/) {
+            cycle_images << file(it)
         }
+        cycle_images.sort()
     }
 
     return [[id:samplesheet_row[index_sample_sample]], cycle_images]