diff --git a/conf/test.config b/conf/test.config
index 5ea319a..dac0e81 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -27,8 +27,6 @@ params {
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
     shortread_qc_mergepairs               = true
-    longread_qc_skipadaptertrim           = false
-    longread_qc_qualityfilter             = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true
diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config
index 0b3e9ce..12c7185 100644
--- a/conf/test_noprofiling.config
+++ b/conf/test_noprofiling.config
@@ -27,8 +27,6 @@ params {
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
     shortread_qc_mergepairs               = true
-    longread_qc_skipadaptertrim           = false
-    longread_qc_qualityfilter             = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true
diff --git a/nextflow.config b/nextflow.config
index 700beef..087c879 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -58,15 +58,15 @@ params {
     perform_shortread_qc             = false
     shortread_qc_tool                = 'fastp'
     shortread_qc_skipadaptertrim     = false
-    shortread_qc_mergepairs          = false
+    shortread_qc_mergepairs          = true
     shortread_qc_excludeunmerged     = false
     shortread_qc_adapter1            = null
     shortread_qc_adapter2            = null
-    shortread_qc_minlength           = 0
+    shortread_qc_minlength           = 15
 
     perform_longread_qc                   = false
     longread_qc_skipadaptertrim           = false
-    longread_qc_qualityfilter             = false
+    longread_qc_qualityfilter             = true
     longread_qc_qualityfilter_minlength   = 1000
     longread_qc_qualityfilter_keeppercent = 90
     longread_qc_qualityfilter_targetbases = 500000000