diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysisExecutor.java index 7e6985a68b..53c7054dfb 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/liftover/LiftoverWrapperAnalysisExecutor.java @@ -1,6 +1,7 @@ package org.opencb.opencga.analysis.wrappers.liftover; import org.apache.commons.lang3.StringUtils; +import org.opencb.commons.datastore.core.Event; import org.opencb.opencga.analysis.wrappers.executors.DockerWrapperAnalysisExecutor; import org.opencb.opencga.core.common.GitRepositoryState; import org.opencb.opencga.core.exceptions.ToolException; @@ -46,6 +47,9 @@ public class LiftoverWrapperAnalysisExecutor extends DockerWrapperAnalysisExecut @Override protected void run() throws Exception { + // Add parameters + addParameters(); + Path outPath = (StringUtils.isEmpty(vcfDest) ? getOutDir() : Paths.get(vcfDest)); int numFails = 0; @@ -90,6 +94,7 @@ private void runLiftover(File file, Path outPath) throws ToolExecutorException { String dockerImage = "opencb/opencga-ext-tools:" + GitRepositoryState.getInstance().getBuildVersion(); String dockerCli = buildCommandLine(dockerImage, inputBindings, outputBinding, params, null); + addEvent(Event.Type.INFO, "Docker command line: " + dockerCli); logger.info("Docker command line: {}", dockerCli); runCommandLine(dockerCli); @@ -119,6 +124,14 @@ private void runLiftover(File file, Path outPath) throws ToolExecutorException { } } + private void addParameters() throws ToolException { + addParam("liftoverPath", liftoverPath); + addParam("files", files); + addParam("targetAssembly", targetAssembly); + addParam("vcfDest", vcfDest); + addParam("resourcePath", resourcePath); + } + public String getStudy() { return study; }