diff --git a/lib/fastqingress.nf b/lib/fastqingress.nf
index 42e6f5c..a353996 100644
--- a/lib/fastqingress.nf
+++ b/lib/fastqingress.nf
@@ -311,7 +311,13 @@ def get_valid_inputs(Map margs){
                 [create_metamap([alias: margs["sample"] ?: input.baseName]), input])
         } else {
             // deal with the second case (sub-directories with fastq data) --> first
-            // check whether we actually found sub-directories
+            // check whether we actually found sub-directories (and remove
+            // sub-directories called 'unclassified' unless otherwise specified)
+            if (!margs.analyse_unclassified) {
+                sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
+                    it.baseName != "unclassified"
+                }
+            }
             if (!sub_dirs_with_fastq_files) {
                 error "Input directory '$input' must contain either FASTQ files " +
                     "or sub-directories containing FASTQ files."
@@ -325,12 +331,6 @@ def get_valid_inputs(Map margs){
                 error "Input directory '$input' cannot contain more " +
                     "than one level of sub-directories with FASTQ files."
             }
-            // remove directories called 'unclassified' unless otherwise specified
-            if (!margs.analyse_unclassified) {
-                sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
-                    it.baseName != "unclassified"
-                }
-            }
             // filter based on sample sheet in case one was provided
             if (margs.sample_sheet) {
                 // get channel of entries in the sample sheet
diff --git a/nextflow.config b/nextflow.config
index f840b6e..c23b403 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -23,7 +23,7 @@ params {
     // filtering + downsampling args
     min_read_length = 300
     max_read_length = null
-    min_read_qual = 10.0
+    min_read_qual = 10
     reads_downsampling_size = null
 
     // mapping + variant calling args
@@ -38,7 +38,7 @@ params {
     aws_image_prefix = null
     aws_queue = null
     disable_ping = false
-    threads = 1
+    threads = 4
 
     // schema etc.
     monochrome_logs = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3489364..d5eee09 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -77,7 +77,7 @@
                 },
                 "min_read_qual": {
                     "type": "number",
-                    "default": 10.0,
+                    "default": 10,
                     "title": "Minimum mean read quality",
                     "description": "Reads with a lower mean quality will be removed."
                 },
@@ -195,12 +195,14 @@
                 },
                 "help": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Display help text.",
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
                 "version": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true