diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java index b190c1b302..2aaced0358 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java @@ -107,7 +107,7 @@ protected void check() throws Exception { if (CollectionUtils.isNotEmpty(workflow.getTags())) { tags.addAll(workflow.getTags()); } -// updateJobInformation(new ArrayList<>(tags), toolInfoExecutor); + updateJobInformation(new ArrayList<>(tags), toolInfoExecutor); this.inputBindings = new LinkedList<>(); if (MapUtils.isNotEmpty(nextflowParams.getParams())) { @@ -189,7 +189,6 @@ protected void run() throws Exception { // Build output binding AbstractMap.SimpleEntry outputBinding = new AbstractMap.SimpleEntry<>(outDirPath, outDirPath); -// String dockerImage = "nextflow/nextflow:" + workflow.getManager().getVersion(); String dockerImage = "opencb/opencga-workflow"; StringBuilder stringBuilder = new StringBuilder() .append("bash -c \"NXF_VER=").append(workflow.getManager().getVersion()).append(" nextflow -c ").append(nextflowConfigPath).append(" run "); @@ -211,10 +210,6 @@ protected void run() throws Exception { stringBuilder.append(" ").append(cliParams); } stringBuilder.append(" -with-report ").append(outDirPath).append("/report.html\""); -// // And give ownership permissions to the user running this process -// stringBuilder.append("; chown -R ") -// .append(UserProcessUtils.getUserUid()).append(":").append(UserProcessUtils.getGroupId()).append(" ").append(outputDir) -// .append("\""); startTraceFileMonitor();