diff --git a/workflow/rules/star_mapping_pass1.rules b/workflow/rules/star_mapping_pass1.rules
index 516ead4a87e0e51dca4486843ee7fce663f0de4a..3929b94624a1859e2acda2b8287cdbd935a5182d 100755
--- a/workflow/rules/star_mapping_pass1.rules
+++ b/workflow/rules/star_mapping_pass1.rules
@@ -45,7 +45,10 @@ rule star_mapping_pass1:
         star_mapping_pass1_logs
     shell:
         """ 
-        if [[ {input.fastq} == "*.gz"  ]]
+        tmp="{input}"
+        infiles=($tmp)
+
+        if [[ ${{infiles[0]}} == "*.gz"  ]]
         then
             STAR --genomeDir {params.index} \
                  --readFilesIn {input.fastq}  \
diff --git a/workflow/rules/star_mapping_pass2.rules b/workflow/rules/star_mapping_pass2.rules
index daae75f7d4cb39c0561106d910b22202c1b2f240..86bf57f7f4709408f133a61083a738a8d30c94ac 100755
--- a/workflow/rules/star_mapping_pass2.rules
+++ b/workflow/rules/star_mapping_pass2.rules
@@ -46,7 +46,10 @@ rule star_mapping_pass2:
         star_mapping_pass2_logs
     shell:
         """ 
-        if [[ {input.fastq} == "*.gz"  ]]
+        tmp="{input}"
+        infiles=($tmp)
+
+        if [[ ${{infiles[0]}} == "*.gz"  ]]
         then
             STAR --genomeDir {params.index} \
                  --readFilesIn {input.fastq}  \