Add --threads flag to bellerophon command (#5424)

* Add --threads flag to bellerophon command * bump version suffix
galaxyproject · Sep 4, 2023 · a4601aa · a4601aa
1 parent 65fa34f
commit a4601aa
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/tools/bellerophon/bellerophon.xml b/tools/bellerophon/bellerophon.xml
@@ -2,7 +2,7 @@
     <description>chimeric reads from Arima Genomics</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement>
@@ -28,6 +28,7 @@
         --reverse $reverse_input
         --quality $quality
         --output 'merged_out.bam'
+        --threads \${GALAXY_SLOTS:-1}
         && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam
         ]]>
     </command>