analysis: add the executor parameters and the docker command line to …

…the JOB result file, #TASK-7064, #TASK-7049

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;
     }