diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 5997fdf137047b6b2c98159e810dc6259d948980..da328807e06772913fc6ba59e0d9eb0ba7493fde 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -101,6 +101,7 @@ fastp --thread ${task.cpus} \
   --out2 ${pair_id}_R2_trim.fastq.gz | \
   fastp --thread ${task.cpus} \
     --stdin \
+    --interleaved_in \
     --trim_front1=10 \
     --trim_front2=10 \
     --qualified_quality_phred 20 \