diff --git a/nextflow.config b/nextflow.config
index 54e220d..00edd9b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -65,7 +65,7 @@ params {
     perform_shortread_qc             = false
     shortread_qc_tool                = 'fastp'
     shortread_qc_skipadaptertrim     = false
-    shortread_qc_mergepairs          = true
+    shortread_qc_mergepairs          = false
     shortread_qc_includeunmerged     = false
     shortread_qc_adapter1            = null
     shortread_qc_adapter2            = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 02085d5..d6debb3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -122,8 +122,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on merging of read pairs for paired-end data",
-                    "default": true,
-                    "help_text": "Turn on the merging of read-pairs of paired-end short read sequencing data for AdapterRemoval (this is performed automatically with fastp).\n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--collapse`\n"
+                    "help_text": "Turn on the merging of read-pairs of paired-end short read sequencing data. \n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--collapse`\n> - fastp: `-m --merged_out`\n"
                 },
                 "shortread_qc_includeunmerged": {
                     "type": "boolean",