Merge pull request #126 from Joon-Klaps/120-set-default-umi-tools-ded…

…up-strategy-to-a-non-read-counting-method set default umitools dedup strategy to 'cluster'
Joon-Klaps · Jun 5, 2024 · 74cfb4f · 74cfb4f
2 parents bdd43ba + 6083b66
commit 74cfb4f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,7 +9,8 @@ Initial release of Joon-Klaps/viralgenie, created with the [nf-core](https://nf-
 
 ### `Enhancement`
 
-- 119 include sspace cobra for contig extension ([#123](https://github.com/Joon-Klaps/viralgenie/pull/123))
+- Set default umitools dedup strategy to cluster ([#126](https://github.com/Joon-Klaps/viralgenie/pull/126))
+- Include sspace for contig extension ([#123](https://github.com/Joon-Klaps/viralgenie/pull/123))
 
 ### `Fixed`
 

diff --git a/nextflow.config b/nextflow.config
@@ -27,7 +27,7 @@ params {
     umi_deduplicate             = 'read'
     humid_mismatches            = 1
     humid_strategy              = 'directional'  // directional vs cluster
-    umitools_dedup_strategy     = 'directional'
+    umitools_dedup_strategy     = 'cluster'
 
     // > Trim
     trim_tool                   = 'fastp'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -107,7 +107,7 @@
                     "fa_icon": "fas fa-project-diagram",
                     "description": "Specify the strategy or method for umi-tools deduplication on mapping level",
                     "enum": ["directional", "unique", "adjacency", "cluster", "percentile"],
-                    "default": "directional"
+                    "default": "cluster"
                 },
                 "umi_discard_read": {
                     "type": "integer",