diff --git a/modules/local/compare_structures.nf b/modules/local/compare_structures.nf
index a8d0629..756d252 100644
--- a/modules/local/compare_structures.nf
+++ b/modules/local/compare_structures.nf
@@ -29,7 +29,7 @@ process COMPARE_STRUCTURES {
         --html_template ${template} \\
         --output_dir ./ \\
         --name ${meta.id} \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/generate_report.nf b/modules/local/generate_report.nf
index 61ccdd1..3bfdc04 100644
--- a/modules/local/generate_report.nf
+++ b/modules/local/generate_report.nf
@@ -26,7 +26,8 @@ process GENERATE_REPORT {
     def args = task.ext.args ?: ''
 
     """
-    generate_report.py --type ${output_type} \\
+    generate_report.py \\
+        --type ${output_type} \\
         --msa ${msa} \\
         --pdb ${pdb.join(' ')} \\
         --html_template ${template} \\