From a026ba147e10833d46968b1b49a291ae3deb0817 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 1 Sep 2023 11:47:08 +0000 Subject: [PATCH] Fix adapter trim for illumina case --- CHANGELOG.md | 1 + lib/WorkflowSmrnaseq.groovy | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ca1a1cc..c9ce51eb 100644 --- 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 index 703c1342..5b94bad7 100755 --- 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':