Merge branch 'fix-BIOPET-425' into 'develop'

Fix biopet 425

Fixes BIOPET-425 and BIOPET-426

See merge request !483

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -68,8 +68,6 @@ object Bam2Wig extends PipelineCommand {
     val bamToBigWig = new Bam2Wig(root)
     bamToBigWig.outputDir = bamFile.getParentFile
     bamToBigWig.bamFile = bamFile
-    bamToBigWig.init()
-    bamToBigWig.biopetScript()
     bamToBigWig
   }
 }
\ No newline at end of file

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -114,6 +114,7 @@ object BamMetricsTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "refFlat" -> "bla.refFlat",
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "samtools" -> Map("exe" -> "test"),

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -144,6 +144,7 @@ object BastyTest {
   copyFile("ref.fa.fai")
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "cache" -> true,
     "dir" -> "test",

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

@@ -36,6 +36,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   var executable: String = _
 
+  var mainFunction = true
+
   /** This is the default shell for drmaa jobs */
   def defaultRemoteCommand = "bash"
   private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)

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

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+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.utils.Logging
@@ -63,6 +63,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
   /** Returns the extension to make the report */
   def reportClass: Option[ReportBuilderExtension] = None
 
+  val skipWriteDependencies: Boolean = config("skip_write_dependencies", default = false)
+
   /** Script from queue itself, final to force some checks for each pipeline and write report */
   final def script() {
     outputDir = config("output_dir")
@@ -85,7 +87,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     this match {
       case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
         logger.info("Write report is skipped because sample flag is used")
-      case _ => reportClass.foreach(add(_))
+      case _ => reportClass.foreach { report =>
+        add(report)
+      }
     }
 
     logger.info("Running pre commands")
@@ -95,7 +99,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
         f.beforeGraph()
         f.internalBeforeGraph()
         f.commandLine
-      case _ =>
+      case f: WriteSummary => f.init()
+      case _               =>
     }
 
     if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
@@ -118,7 +123,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
-    if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
+    if (!skipWriteDependencies) 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

@@ -16,9 +16,11 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.{ File, PrintWriter }
 
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import org.broadinstitute.gatk.queue.function.{ CommandLineFunction, QFunction }
+
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 
@@ -37,7 +39,7 @@ object WriteDependencies extends Logging with Configurable {
         case f               => f.getClass.getSimpleName
       }
       cache += baseName -> (cache.getOrElse(baseName, 0) + 1)
-      function -> s"$baseName-${cache(baseName)}"
+      function -> s"${baseName.replaceAll("-", "_")}_${cache(baseName)}"
     }).toMap
   }
 
@@ -45,9 +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): 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)
@@ -107,27 +110,89 @@ object WriteDependencies extends Logging with Configurable {
 
     val jobs = functionNames.par.map {
       case (f, name) =>
-        name -> Map("command" -> (f match {
+        name.toString -> Map("command" -> (f match {
           case cmd: CommandLineFunction => cmd.commandLine
           case _                        => None
+        }), "main_job" -> (f match {
+          case cmd: BiopetCommandLineFunction            => cmd.mainFunction
+          case s: WriteSummary if s.qscript.root == null => true
+          case _                                         => false
         }), "intermediate" -> f.isIntermediate,
           "depends_on_intermediate" -> f.inputs.exists(files(_).isIntermediate),
           "depends_on_jobs" -> f.inputs.toList.flatMap(files(_).outputJobNames).distinct,
           "output_used_by_jobs" -> outputFiles(f).toList.flatMap(files(_).inputJobNames).distinct,
           "outputs" -> outputFiles(f).toList,
           "inputs" -> f.inputs.toList,
+          "done_files" -> f.doneOutputs.toList,
+          "fail_files" -> f.failOutputs.toList,
+          "stdout_file" -> f.jobOutputFile,
           "done_at_start" -> f.isDone,
           "fail_at_start" -> f.isFail)
     }.toIterator.toMap
 
+    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(
-      "jobs" -> jobs.toMap,
+      "jobs" -> jobs,
       "files" -> files.values.par.map(_.getMap).toList
     )).spaces2)
     writer.close()
 
+    val jobsDeps = jobs.map(x => x._1 -> (x._2("depends_on_jobs") match {
+      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"$prefix.jobs.json"))
+    jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)
+    jobsWriter.close()
+    writeGraphvizFile(jobsDeps, new File(outputDir, s"$prefix.jobs.gv"))
+    writeGraphvizFile(compressOnType(jobsDeps), new File(outputDir, s"$prefix.compress.jobs.gv"))
+
+    val mainJobs = jobs.filter(_._2("main_job") == true).map {
+      case (name, job) =>
+        name -> getMainDependencies(name, jobs)
+    }
+
+    val mainJobsWriter = new PrintWriter(new File(outputDir, s"$prefix.main_jobs.json"))
+    mainJobsWriter.println(ConfigUtils.mapToJson(mainJobs).spaces2)
+    mainJobsWriter.close()
+    writeGraphvizFile(mainJobs, new File(outputDir, s"$prefix.main_jobs.gv"))
+    writeGraphvizFile(compressOnType(mainJobs), new File(outputDir, s"$prefix.compress.main_jobs.gv"))
+
     logger.info("done calculating dependencies")
   }
+
+  def getMainDependencies(jobName: String, jobsMap: Map[String, Map[String, Any]]): List[String] = {
+    val job = jobsMap(jobName)
+    val dependencies = job("depends_on_jobs") match {
+      case l: List[_] => l.map(_.toString)
+    }
+    dependencies.flatMap { dep =>
+      jobsMap(dep)("main_job") match {
+        case true  => List(dep)
+        case false => getMainDependencies(dep, jobsMap)
+      }
+    }.distinct
+  }
+
+  val numberRegex = """(.*)_(\d*)$""".r
+  def compressOnType(jobs: Map[String, List[String]]): Map[String, List[String]] = {
+    val set = for ((job, deps) <- jobs.toSet; dep <- deps) yield {
+      job match {
+        case numberRegex(name, number) => (name, dep match {
+          case numberRegex(name, number) => name
+        })
+      }
+    }
+    set.groupBy(_._1).map(x => x._1 -> x._2.map(_._2).toList)
+  }
+
+  def writeGraphvizFile(jobs: Map[String, List[String]], outputFile: File): Unit = {
+    val writer = new PrintWriter(outputFile)
+    writer.println("digraph graphname {")
+    jobs.foreach { case (a, b) => b.foreach(c => writer.println(s"  $c -> $a;")) }
+    writer.println("}")
+    writer.close()
+  }
 }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for md5sum */
 class Md5sum(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  mainFunction = false
+
   @Input(doc = "Input")
   var input: File = _
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -49,15 +49,23 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
   //TODO: add more checksums types
 
   override def freezeFieldValues(): Unit = {
-    for (q <- qscript.summaryQScripts) deps :+= q.summaryFile
+    init()
+    super.freezeFieldValues()
+  }
+
+  def init(): Unit = {
+    for (q <- qscript.summaryQScripts)
+      deps :+= q.summaryFile
     for ((_, l) <- qscript.summarizables; s <- l) s match {
-      case f: QFunction => deps :+= f.firstOutput
+      case f: QFunction => try {
+        deps :+= f.firstOutput
+      }  catch {
+        case e: NullPointerException => logger.warn("Queue values are not init")
+      }
       case _            =>
     }
 
     jobOutputFile = new File(out.getParentFile, ".%s.%s.out".format(out.getName, analysisName))
-
-    super.freezeFieldValues()
   }
 
   /** Function to create summary */

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")

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

@@ -30,6 +30,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 class SeqStat(val root: Configurable) extends ToolCommandFunction with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
 
+  mainFunction = false
+
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
   var input: File = null
 

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala

@@ -32,6 +32,8 @@ import scala.io.Source
 class VcfStats(val root: Configurable) extends ToolCommandFunction with Summarizable with Reference {
   def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
 
+  mainFunction = false
+
   @Input(doc = "Input fastq", shortName = "I", required = true)
   var input: File = _
 

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -117,6 +117,7 @@ object CarpTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -115,6 +115,7 @@ object FlexiprepTest {
   Files.touch(r2Zipped)
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "seqstat" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala

@@ -51,7 +51,8 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     centrifugeKreport.centrifugeOutputFiles :+= fifo
     centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
     centrifugeKreport.onlyUnique = unique
-    add(new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo))))
+    val pipe = new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo)))
+    add(pipe)
 
     val krakenReportJSON = new KrakenReportToJson(this)
     krakenReportJSON.inputReport = centrifugeKreport.output

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -234,6 +234,7 @@ object TestGearsSingle {
   bam.deleteOnExit()
 
   val executables = Map(
+    "skip_write_dependencies" -> true,
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "centrifuge" -> Map("exe" -> "test", "centrifuge_index" -> "test"),
     "centrifugekreport" -> Map("exe" -> "test"),

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -113,6 +113,7 @@ object GearsTest {
   Files.touch(bam)
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "output_dir" -> outputDir,
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala

@@ -141,7 +141,9 @@ object DownloadGenomesTest {
   val outputDir = Files.createTempDir()
   outputDir.deleteOnExit()
 
-  val config = Map("output_dir" -> outputDir,
+  val config = Map(
+    "skip_write_dependencies" -> true,
+    "output_dir" -> outputDir,
     "bwa" -> Map("exe" -> "test"),
     "star" -> Map("exe" -> "test"),
     "hisat2build" -> Map("exe" -> "test"),

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -186,6 +186,7 @@ object GentrapTest {
   copyFile("ref.fa.fai")
 
   val executables: Map[String, Any] = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "refFlat" -> (outputDir + File.separator + "ref.fa"),
     "annotation_gtf" -> (outputDir + File.separator + "ref.fa"),

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -75,6 +75,7 @@ object GwasTestTest {
   }
 
   val config = Map(
+    "skip_write_dependencies" -> true,
     "reference_fasta" -> reference.toString,
     "phenotype_file" -> phenotypeFile.toString,
     "output_dir" -> outputDir,

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -93,6 +93,7 @@ object I