diff --git a/src/nf_modules/porechop/main.nf b/src/nf_modules/porechop/main.nf
index 979db858e845f49353eaf5f532692c4d689aaf33..579a9e4bb874c2981fbf092cf14cef3589769862 100755
--- a/src/nf_modules/porechop/main.nf
+++ b/src/nf_modules/porechop/main.nf
@@ -19,6 +19,6 @@ process porechop {
 """
 mkdir ${barcode}
 cd ${barcode}/
-porechop --input ../${fastq} -o ${barcode}_merged_porechoped.fastq.gz --threads ${task.cpus}
+porechop --input \$(readlink -f ../${fastq}) -o ${barcode}_merged_porechoped.fastq.gz --threads ${task.cpus}
 """
 }
\ No newline at end of file