Merge branch 'dev' of https://github.com/Joon-Klaps/viralgenie into dev

Author: Joon-Klaps

conf/tests/test_umi.config

@@ -29,8 +29,6 @@ params {
     skip_complexity_filtering   = false
     trim_tool                   ='fastp'
     with_umi                    = true
-    fastp_deduplicate           = true
-    fastp_dedup_accuracy        = 2
     skip_umi_extract            = false
     umi_deduplicate             = 'both'
     host_k2_db                  = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/kraken2/kraken2_hs22.tar.gz'
@@ -49,11 +47,5 @@ params {
     intermediate_mapping_stats  = true
     min_mapped_reads            = 100
     skip_checkv                 = true
-}
-
-process{
-    withName: UMITOOLS_EXTRACT {
-        ext.args = '--bc-pattern="NNNN"'
-    }
-    maxRetries    = 1
+    arguments_umitools_extract  = '--bc-pattern="NNNN"'
 }