diff --git a/poreCov.nf b/poreCov.nf
index 833e8c4..872f0b7 100755
--- a/poreCov.nf
+++ b/poreCov.nf
@@ -112,7 +112,7 @@ if ( params.single && params.samples ) { exit 1, "Sample input [--samples] not s
 
 // check that input params are used as such
 if (params.fasta == true) { exit 5, "Please provide a fasta file via [--fasta]" }
-if (params.fastq == true) { exit 5, "Please provide a fastq files (one per sample) via [--fastq]" }
+if (params.fastq == true && !params.list) { exit 5, "Please provide a fastq files (one per sample) via [--fastq]" }
 if (params.fastq_pass == true) { exit 5, "Please provide a fastq_pass dir via [--fastq_pass]" }
 if (params.fast5 == true) { exit 5, "Please provide a fast5 dir via [--fast5]" }
 if (params.minLength && !params.minLength.toString().matches("[0-9]+")) { exit 5, "Please provide an integer number (e.g. 300) as minimal read length via [--minLength]" }