diff --git a/tests/run.config b/tests/run.config
index fc15787..2de10f1 100644
--- a/tests/run.config
+++ b/tests/run.config
@@ -15,6 +15,9 @@ params {
     sample_sheet = "${projectDir}/test-data/samplesheet.csv" // Path to library TSV
     adapters = "${projectDir}/ref/adapters.fasta" // Path to adapter file for adapter trimming
 
+    // Whether the underlying data is paired-end or single-end
+    single_end = new File(params.sample_sheet).text.readLines()[0].contains('fastq_2') ? false : true
+
     // Numerical
     grouping = false // Whether to group samples by 'group' column in samplesheet
     n_reads_trunc = 0 // Number of reads per sample to run through pipeline (0 = all reads)