Merge pull request #276 from nf-core/fix-illumina-adapters

nf-core · Sep 1, 2023 · d25cc4f · d25cc4f
2 parents 2b4253f + a026ba1
commit d25cc4f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01
 
 - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers
+- [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default
 
 ## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12
 

diff --git a/lib/WorkflowSmrnaseq.groovy b/lib/WorkflowSmrnaseq.groovy
@@ -125,8 +125,8 @@ class WorkflowSmrnaseq {
 
         switch(params.protocol){
             case 'illumina':
-                params.putIfAbsent("clip_r1", 1);
-                params.putIfAbsent("three_prime_clip_r1",2);
+                params.putIfAbsent("clip_r1", 0);
+                params.putIfAbsent("three_prime_clip_r1",0);
                 params.putIfAbsent("three_prime_adapter", "TGGAATTCTCGGGTGCCAAGG");
                 break
             case 'nextflex':