diff --git a/hmftools.wdl b/hmftools.wdl index 3fe845a689b21be4c6d1438934e3ea5d3fd71135..49e4eeb4f95ec1fc973d0e85abf49de3026429d2 100644 --- a/hmftools.wdl +++ b/hmftools.wdl @@ -590,9 +590,7 @@ task Sage { } command { - java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \ - -cp /usr/local/share/hmftools-sage-2.2-2/sage.jar \ - com.hartwig.hmftools.sage.SageApplication \ + SAGE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \ -tumor ~{tumorName} \ -tumor_bam ~{tumorBam} \ ~{"-reference " + normalName} \