Apply JVM heap space modifier to VIRUSBreakend

nf-core · Nov 8, 2024 · 8f2a24f · 8f2a24f
1 parent 9caa5b0
commit 8f2a24f
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf
@@ -27,13 +27,15 @@ process VIRUSBREAKEND {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     """
     # Symlink indices next to assembly FASTA
     ln -s \$(find -L ${genome_gridss_index} -regex '.*\\.\\(amb\\|ann\\|pac\\|gridsscache\\|sa\\|bwt\\|img\\|alt\\)') ./
 
     virusbreakend \\
         ${args} \\
-        --gridssargs "--jvmheap ${Math.round(task.memory.bytes * 0.95)}" \\
+        --gridssargs "--jvmheap ${Math.round(task.memory.bytes * xmx_mod)}" \\
         --threads ${task.cpus} \\
         --db ${virusbreakenddb.toString().replaceAll("/\$", "")}/ \\
         --output ${meta.sample_id}.virusbreakend.vcf \\