analysis: write trace.txt in output directory, #TASK-6445

Author: pfurio

opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java

@@ -31,11 +31,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.io.UncheckedIOException;
+import java.io.*;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.*;
@@ -197,7 +197,7 @@ protected void run() throws Exception {
         Path nextflowConfigPath;
         if (nextflowConfig != null) {
             nextflowConfigPath = temporalInputDir.resolve("nextflow.config");
-            Files.copy(nextflowConfig.openStream(), nextflowConfigPath);
+            writeNextflowConfigFile(Paths.get(nextflowConfig.toURI()), nextflowConfigPath, outDirPath);
             dockerInputBindings.add(new AbstractMap.SimpleEntry<>(nextflowConfigPath.toString(), nextflowConfigPath.toString()));
         } else {
             throw new RuntimeException("Can't fetch nextflow.config file");
@@ -236,8 +236,8 @@ protected void run() throws Exception {
         // when nextflow runs on other dockers, we need to store those files in a path shared between the parent docker and the host
         dockerParams.put("-e", "HOME=" + temporalInputDir);
         dockerParams.put("-e", "OPENCGA_TOKEN=" + getExpiringToken());
-        // Disable user param
-        dockerParams.put("user", "");
+        // Set user uid and guid to 1001
+        dockerParams.put("user", "1001:1001");
 
         // Execute docker image
         StopWatch stopWatch = StopWatch.createStarted();
@@ -257,6 +257,22 @@ protected void close() {
         deleteTemporalFiles();
     }
 
+    private void writeNextflowConfigFile(Path inputFile, Path outputFile, String outdirPath) {
+        try (BufferedReader reader = Files.newBufferedReader(inputFile);
+             BufferedWriter writer = Files.newBufferedWriter(outputFile)) {
+
+            String line;
+            while ((line = reader.readLine()) != null) {
+                // Replace occurrences of "$OUTPUT" with the replacement string
+                line = line.replace("$OUTPUT", outdirPath);
+                writer.write(line);
+                writer.newLine();
+            }
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
     private void deleteTemporalFiles() {
         // Delete temporal files and folders created by nextflow
         try (Stream<Path> paths = Files.walk(getOutDir().resolve(".nextflow"))) {

opencga-analysis/src/main/resources/nextflow.config

@@ -1,6 +1,6 @@
 trace {
     enabled = true
-    file = '/data/output/trace.txt'
+    file = '$OUTPUT/trace.txt'
     overwrite = true
     fields = 'task_id,hash,name,status,start,complete,%cpu,peak_vmem'
 }