Added a jobs file

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -121,10 +121,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
-    WriteDependencies.writeDependencies(functions,
-      new File(outputDir, s".log/${qSettings.runName}.deps.json"),
-      Some(new File(outputDir, s".log/${qSettings.runName}.mainJobs.json"))
-    )
+    WriteDependencies.writeDependencies(functions, new File(outputDir, ".log"), qSettings.runName)
 
     Logging.checkErrors()
     logger.info("Script complete without errors")

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -47,9 +47,10 @@ object WriteDependencies extends Logging with Configurable {
    * This method will generate a json file where information about job and file dependencies are stored
    *
    * @param functions This should be all functions that are given to the graph of Queue
-   * @param outputFile Json file to write dependencies to
+   * @param outputDir
+   * @param prefix prefix
    */
-  def writeDependencies(functions: Seq[QFunction], outputFile: File, mainJobsFile: Option[File] = None): Unit = {
+  def writeDependencies(functions: Seq[QFunction], outputDir: File, prefix: String): Unit = {
     logger.info("Start calculating dependencies")
 
     val errorOnMissingInput: Boolean = config("error_on_missing_input", false)
@@ -126,17 +127,7 @@ object WriteDependencies extends Logging with Configurable {
           "fail_at_start" -> f.isFail)
     }.toIterator.toMap
 
-    mainJobsFile.foreach { file =>
-      val mainJobs = jobs.filter(_._2("main_job") == true).map {
-        case (name, job) =>
-          name -> getMainDependencies(name, jobs)
-      }
-
-      val writer = new PrintWriter(file)
-      writer.println(ConfigUtils.mapToJson(mainJobs).spaces2)
-      writer.close()
-    }
-
+    val outputFile = new File(outputDir, s"$prefix.deps.json")
     logger.info(s"Writing dependencies to: $outputFile")
     val writer = new PrintWriter(outputFile)
     writer.println(ConfigUtils.mapToJson(Map(
@@ -145,6 +136,20 @@ object WriteDependencies extends Logging with Configurable {
     )).spaces2)
     writer.close()
 
+    val jobsDeps = jobs.map(x => x._1 -> (x._2("depends_on_jobs")))
+    val jobsWriter = new PrintWriter(new File(outputDir, s"$prefix.jobs.json"))
+    jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)
+    jobsWriter.close()
+
+    val mainJobs = jobs.filter(_._2("main_job") == true).map {
+      case (name, job) =>
+        name -> getMainDependencies(name, jobs)
+    }
+
+    val mainJobsWriter = new PrintWriter(new File(outputDir, s"$prefix.main_jobs.json"))
+    mainJobsWriter.println(ConfigUtils.mapToJson(mainJobs).spaces2)
+    mainJobsWriter.close()
+
     logger.info("done calculating dependencies")
   }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala

@@ -15,16 +15,14 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.File
-import java.nio.file.Files
 
+import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-import scala.io.Source
-
 /**
  * Created by pjvanthof on 09/05/16.
  */
@@ -42,11 +40,14 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
 
   @Test
   def testDeps: Unit = {
-    val outputFile = File.createTempFile("deps.", ".json")
+    val tempDir = Files.createTempDir()
+    tempDir.deleteOnExit()
+    val prefix = "test"
+    val outputFile = new File(tempDir, s"$prefix.deps.json")
     outputFile.deleteOnExit()
     val func1 = Qfunc(file1 :: Nil, file2 :: Nil)
     val func2 = Qfunc(file2 :: Nil, file3 :: Nil)
-    WriteDependencies.writeDependencies(func1 :: func2 :: Nil, outputFile)
+    WriteDependencies.writeDependencies(func1 :: func2 :: Nil, tempDir, prefix)
     val deps = ConfigUtils.fileToConfigMap(outputFile)
     deps("jobs") shouldBe a[Map[_, _]]
     val jobs = deps("jobs").asInstanceOf[Map[String, Map[String, Any]]]
@@ -66,7 +67,7 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
 }
 
 object WriteDependenciesTest {
-  val tempDir = Files.createTempDirectory("test").toFile
+  val tempDir = Files.createTempDir()
   tempDir.deleteOnExit()
   val file1 = new File(tempDir, "file1.txt")
   val file2 = new File(tempDir, "file2.txt")