Move graph files

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

@@ -16,13 +16,14 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, WriteSummary }
+import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, WriteSummary}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
+import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.queue.{ QScript, QSettings }
+import org.broadinstitute.gatk.queue.{QScript, QSettings}
 import org.broadinstitute.gatk.queue.function.QFunction
-import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
 
 /** Base for biopet pipeline */
 trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
@@ -123,7 +124,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
-    if (!skipWriteDependencies) WriteDependencies.writeDependencies(functions, new File(outputDir, ".log"), qSettings.runName)
+    if (!skipWriteDependencies) WriteDependencies.writeDependencies(
+      functions,
+      new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp + File.separator + "graph"))
 
     Logging.checkErrors()
     logger.info("Script complete without errors")

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

@@ -48,9 +48,8 @@ object WriteDependencies extends Logging with Configurable {
    *
    * @param functions This should be all functions that are given to the graph of Queue
    * @param outputDir
-   * @param prefix prefix
    */
-  def writeDependencies(functions: Seq[QFunction], outputDir: File, prefix: String): Unit = {
+  def writeDependencies(functions: Seq[QFunction], outputDir: File): Unit = {
     logger.info("Start calculating dependencies")
 
     val errorOnMissingInput: Boolean = config("error_on_missing_input", false)
@@ -130,7 +129,7 @@ object WriteDependencies extends Logging with Configurable {
           "fail_at_start" -> f.isFail)
     }.toIterator.toMap
 
-    val outputFile = new File(outputDir, s"$prefix.deps.json")
+    val outputFile = new File(outputDir, s"deps.json")
     logger.info(s"Writing dependencies to: $outputFile")
     val writer = new PrintWriter(outputFile)
     writer.println(ConfigUtils.mapToJson(Map(
@@ -143,22 +142,22 @@ object WriteDependencies extends Logging with Configurable {
       case l: List[_] => l.map(_.toString)
       case _          => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
     }))
-    val jobsWriter = new PrintWriter(new File(outputDir, s"$prefix.jobs.json"))
+    val jobsWriter = new PrintWriter(new File(outputDir, s"jobs.json"))
     jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)
     jobsWriter.close()
-    writeGraphvizFile(jobsDeps, new File(outputDir, s"$prefix.jobs.gv"))
-    writeGraphvizFile(compressOnType(jobsDeps), new File(outputDir, s"$prefix.compress.jobs.gv"))
+    writeGraphvizFile(jobsDeps, new File(outputDir, s"jobs.gv"))
+    writeGraphvizFile(compressOnType(jobsDeps), new File(outputDir, s"compress.jobs.gv"))
 
     val mainJobs = jobs.filter(_._2("main_job") == true).map {
       case (name, job) =>
         name -> getMainDependencies(name, jobs)
     }
 
-    val mainJobsWriter = new PrintWriter(new File(outputDir, s"$prefix.main_jobs.json"))
+    val mainJobsWriter = new PrintWriter(new File(outputDir, s"main_jobs.json"))
     mainJobsWriter.println(ConfigUtils.mapToJson(mainJobs).spaces2)
     mainJobsWriter.close()
-    writeGraphvizFile(mainJobs, new File(outputDir, s"$prefix.main_jobs.gv"))
-    writeGraphvizFile(compressOnType(mainJobs), new File(outputDir, s"$prefix.compress.main_jobs.gv"))
+    writeGraphvizFile(mainJobs, new File(outputDir, s"main_jobs.gv"))
+    writeGraphvizFile(compressOnType(mainJobs), new File(outputDir, s"compress.main_jobs.gv"))
 
     logger.info("done calculating dependencies")
   }