diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf index ae262ef8..2dee6d8b 100644 --- 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 \\