Merge pull request #679 from d4straub/fix-vsearch-cluster

Prevent masking low complexity regions by VSEARCH
nf-core · Dec 19, 2023 · de53107 · de53107
2 parents a86f9c7 + 55116e0
commit de53107
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables
 - [#673](https://github.com/nf-core/ampliseq/pull/673) - Fix logic relating to generation of qiime2 taxonomy part of summary report
 - [#676](https://github.com/nf-core/ampliseq/pull/676) - Phyloseq sometimes only produced one of multiple output files
+- [#679](https://github.com/nf-core/ampliseq/pull/679) - Prevent masking low complexity regions by VSEARCH with lower case letters
 
 ### `Dependencies`
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -451,7 +451,7 @@ process {
     }
 
     withName: VSEARCH_CLUSTER {
-        ext.args = "--id ${params.vsearch_cluster_id} --usersort"
+        ext.args = "--id ${params.vsearch_cluster_id} --usersort --qmask 'none'"
         ext.args2 = '--cluster_smallmem'
         ext.args3 = '--clusters'
     }