diff --git a/tools/salmon/alevin.xml b/tools/salmon/alevin.xml
index fe645f2b02..8fd5142f97 100644
--- a/tools/salmon/alevin.xml
+++ b/tools/salmon/alevin.xml
@@ -326,7 +326,7 @@
                 <param name="strandedness" value="SR"/>
             </conditional>
             <conditional name="protocol_cond">
-                <param name="protocol" value="-\-indropV2"/>
+                <param name="protocol" value="--indropV2"/>
                 <param name="w1" value="ATCAT"/>
             </conditional>
             <param name="tgmap" value="minitxp.tsv"/>
diff --git a/tools/salmon/macros.xml b/tools/salmon/macros.xml
index 89ca3c6047..2df171384e 100644
--- a/tools/salmon/macros.xml
+++ b/tools/salmon/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@IDX_VERSION@">q7</token>
     <token name="@PROFILE_VERSION@">20.01</token>
     <xml name="xrefs">
@@ -414,6 +414,7 @@
         #end if
 
         salmon quant
+            --no-version-check
             --index '$index_path'
             #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
                 --libType ${quant_type.input.single_or_paired.libtype.strandedness}