diff --git a/conf/modules.config b/conf/modules.config
index 32024d9..905d6f2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -339,6 +339,7 @@ process {
                 mode: params.publish_dir_mode,
                 enabled: params.perform_shortread_hostremoval,
                 pattern: '*.fastq.gz',
+                // Don't know why `!` doesn't work here, but `== false` makes it work...
                 saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
             ]
         ]
@@ -381,9 +382,10 @@ process {
             [
                 path: { "${params.outdir}/analysis_ready_fastqs" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fastq.gz',
+                pattern: '*.fq.gz',
                 enabled: params.save_analysis_ready_fastqs,
-                saveAs: { ( !params.perform_runmerging | params.perform_runmerging && !meta.is_multirun ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
+                // Don't know why `!` doesn't work here, but `== false` makes it work...
+                saveAs: { ( !params.perform_runmerging || params.perform_runmerging && !meta.is_multirun ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
             ]
         ]
     }