diff --git a/main.nf b/main.nf
index 9ba5a19..5b5f7ae 100644
--- a/main.nf
+++ b/main.nf
@@ -89,7 +89,7 @@ def get_project_and_reads(run_folder) {
     Channel
         .fromPath("${run_folder}/${params.demultiplexer_outdir}/**.fastq.gz")
         .filter { file -> file.name =~ /.*_[^I]\d_001\.fastq\.gz$/ }
-        .filter { file -> file.size() > 0 }
+        .filter { file -> file.size() > 100 } // An empty gzip file is ~ 50 bytes in size
         .ifEmpty { error "Error: No fastq files found under ${run_folder}/!" }
         .map { file ->
             file.toString().indexOf('Undetermined') > 0 ?
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz
index e69de29..5c253f8 100644
Binary files a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz and b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz differ
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz
index e69de29..338bb83 100644
Binary files a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz and b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz differ