Merge pull request #42 from nf-core/clahe_prefix_fix

Clahe prefix fix
nf-core · Dec 18, 2023 · 6c1eef8 · 6c1eef8
2 parents eecf921 + 6967c92
commit 6c1eef8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1dev - [2023.12.18]
+
+### `Fixed`
+
+- Changed file prefix used in CLAHE to prevent file naming collisions if user used dots in filenames
+
 ## v1.0.1dev - [2023.12.15]
 
 ### `Added`

diff --git a/conf/modules.config b/conf/modules.config
@@ -162,7 +162,11 @@ process {
     }
 
     withName: "CLAHE" {
-        ext.prefix = { "${meta.id}_${image.name.split("\\.")[0]}_clahe" }
+        ext.prefix = {
+            def name = image.name
+            def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name
+            return "${meta.id}_${base}_clahe"
+        }
         ext.when  = { !params.skip_clahe }
         ext.args  = [ "",
             params.clahe_pyramid_tile ? "--tile-size ${params.clahe_pyramid_tile}" : "",