diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 4228dc5f272a7a118ef36efe1f2562fdb5b4ce94..1a402ba50b5f243c0258323f8c511b2f1f7821e3 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -18,7 +18,13 @@ process index_fasta {
 
   script:
 """
-samtools faidx ${params.index_fasta} ${fasta}
+if gzip -t file.gz; then
+  zcat ${fasta} > ${fasta.simpleName}.fasta
+  samtools faidx ${params.index_fasta}  ${fasta.simpleName}.fasta
+else
+  samtools faidx ${params.index_fasta} ${fasta}
+fi
+
 """
 }