Merge branch 'develop' into feature-docs-0.6.0

docs/general/config.md

@@ -47,16 +47,24 @@ For BAM files as input one should use a config like this:
 ``` yaml
 samples:
   Sample_ID_1:
+    tags:
+      gender: male
+      father: sampleNameFather
+      mother: sampleNameMother
     libraries:  
       Lib_ID_1:
+        tags:
+          key: value
         bam: MyFirst.bam
       Lib_ID_2:
         bam: MySecond.bam
 ```
 
-
 Note that there is a tool called [SamplesTsvToJson](../tools/SamplesTsvToJson.md) this enables a user to get the sample config without any chance of creating a wrongly formatted JSON file.
 
+#### Tags
+
+In the `tags` key inside a sample or library users can supply tags that belong to samples/libraries. These tags will we automatically parsed inside the summary of a pipeline.
 
 ### The settings config
 The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.

docs/tools/SamplesTsvToJson.md

@@ -21,12 +21,18 @@ Usage: SamplesTsvToJson [options]
         Print version
   -i <file> | --inputFiles <file>
         Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed
+  -t <file> | --tagFiles <file>
+
+  -o <file> | --outputFile <file>
+
 ~~~
 
 The tool is designed in such a way that a user can provide a TAB seperated file (TSV) with sample specific properties and even those will be parsed by the tool.
 For example: a user wants to have certain properties e.g. which treatment a sample got than the user should provide a extra columns called treatment and then the 
 JSON file is parsed with those properties inside it as well. The order of columns does not matter.
 
+The tag files works the same only the value are prefixed in the key `tags`.
+
 #### Example
 
 ~~~ json

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -194,10 +194,11 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
   protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
 
   protected lazy val nameRegex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
-  protected lazy val nameError = " name invalid." +
-    "Name must have at least 3 characters," +
+  protected lazy val nameError = "has an invalid name. " +
+    "Sample names must have at least 3 characters, " +
     "must begin and end with an alphanumeric character, " +
-    "and must not have whitespace."
+    "and must not have whitespace and special characters. " +
+    "Dash (-) and underscore (_) are permitted."
 
   /** Runs addAndTrackJobs method for each sample */
   final def addSamplesJobs() {

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -19,8 +19,8 @@ import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.utils.Logging
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 
 import scala.collection.JavaConversions._
 
@@ -69,16 +69,40 @@ trait Reference extends Configurable {
   /** Returns the fasta file */
   def referenceFasta(): File = {
     val file: File = config("reference_fasta")
-    checkFasta(file)
-
-    val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta").stripSuffix(".fna") + ".dict")
-    val fai = new File(file.getAbsolutePath + ".fai")
-
-    this match {
-      case c: BiopetCommandLineFunction => c.deps :::= dict :: fai :: Nil
-      case _                            =>
+    if (config.contains("reference_fasta")) {
+      checkFasta(file)
+
+      val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta").stripSuffix(".fna") + ".dict")
+      val fai = new File(file.getAbsolutePath + ".fai")
+
+      this match {
+        case c: BiopetCommandLineFunction => c.deps :::= dict :: fai :: Nil
+        case _                            =>
+      }
+    } else {
+      val defaults = ConfigUtils.mergeMaps(this.defaults, this.internalDefaults)
+
+      def getReferences(map: Map[String, Any]): Set[(String, String)] = (for (
+        (species, species_content: Map[String, Any]) <- map.getOrElse("references", Map[String, Any]()).asInstanceOf[Map[String, Any]].toList;
+        (reference_name, _) <- species_content.toList
+      ) yield (species, reference_name)).toSet
+
+      val references = getReferences(defaults) ++ getReferences(Config.global.map)
+      if (!references.contains((referenceSpecies, referenceName))) {
+        val buffer = new StringBuilder()
+        if (references.exists(_._1 == referenceSpecies)) {
+          buffer.append(s"Reference: '$referenceName' does not exist in config for species: '$referenceSpecies'")
+          buffer.append(s"\nRefrences found for species '$referenceSpecies':")
+          references.filter(_._1 == referenceSpecies).foreach(x => buffer.append("\n - " + x._2))
+        } else {
+          buffer.append(s"Species: '$referenceSpecies' does not exist in config")
+          if (references.nonEmpty) buffer.append("\n    References available in config (species -> reference_name):")
+          else buffer.append("\n    No references found in user or global config")
+          references.toList.sorted.foreach(x => buffer.append(s"\n     - ${x._1} -> ${x._2}"))
+        }
+        Logging.addError(buffer.toString)
+      }
     }
-
     file
   }
 
@@ -117,6 +141,7 @@ object Reference {
 
   /**
    * Raise an exception when given fasta file has no fai file
+   *
    * @param fastaFile Fasta file
    */
   def requireFai(fastaFile: File): Unit = {
@@ -132,6 +157,7 @@ object Reference {
 
   /**
    * Raise an exception when given fasta file has no dict file
+   *
    * @param fastaFile Fasta file
    */
   def requireDict(fastaFile: File): Unit = {

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

@@ -24,7 +24,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   @Input(doc = "Python script", required = false)
   var python_script: File = _
 
-  executable = config("exe", default = "python", submodule = "python")
+  executable = config("exe", default = "python", submodule = "python", freeVar = false)
 
   protected var python_script_name: String = _
 

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -93,9 +93,9 @@ trait ReportBuilder extends ToolCommand {
   private var total = 0
 
   private var _sampleId: Option[String] = None
-  protected def sampleId = _sampleId
+  protected[report] def sampleId = _sampleId
   private var _libId: Option[String] = None
-  protected def libId = _libId
+  protected[report] def libId = _libId
 
   case class ExtFile(resourcePath: String, targetPath: String)
 
@@ -152,6 +152,8 @@ trait ReportBuilder extends ToolCommand {
     total = ReportBuilder.countPages(indexPage)
     logger.info(total + " pages to be generated")
 
+    done = 0
+
     logger.info("Generate pages")
     val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
       args = pageArgs ++ cmdArgs.pageArgs.toMap ++
@@ -216,7 +218,7 @@ object ReportBuilder {
   protected val engine = new TemplateEngine()
 
   /** Cache of temp file for templates from the classpath / jar */
-  private var templateCache: Map[String, File] = Map()
+  private[report] var templateCache: Map[String, File] = Map()
 
   /** This will give the total number of pages including all nested pages */
   def countPages(page: ReportPage): Int = {

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

@@ -112,11 +112,15 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
             Map("samples" -> q.samples.map {
               case (sampleName, sample) =>
                 sampleName -> Map(
-                  qscript.summaryName -> Map("settings" -> sample.summarySettings),
+                  qscript.summaryName -> Map(
+                    "settings" -> sample.summarySettings,
+                    "tags" -> sample.sampleTags),
                   "libraries" -> sample.libraries.map {
                     case (libName, lib) =>
                       libName -> Map(
-                        qscript.summaryName -> Map("settings" -> lib.summarySettings)
+                        qscript.summaryName -> Map(
+                          "settings" -> lib.summarySettings,
+                          "tags" -> lib.libTags)
                       )
                   }
                 )

public/biopet-core/src/test/resources/empty_summary.json

+{
+  "samples": {
+    "sampleName": {
+      "libraries": {
+        "libName": {
+
+        }
+      }
+    }
+  }
+}
\ No newline at end of file

public/biopet-core/src/test/resources/template.ssp

+<%@ var arg: String%>
+${arg}
\ No newline at end of file

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala

@@ -4,13 +4,14 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QScript
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
+import scala.language.reflectiveCalls
 import scala.collection.mutable.ListBuffer
 
 /**
@@ -90,6 +91,20 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
 
     script.functions.size shouldBe 1
   }
+
+  @Test
+  def testInvalidSampleName: Unit = {
+    val script = MultiSampleQScriptTest(sample4 :: Nil)
+    script.init()
+    script.biopetScript()
+    val msg = script.getLastLogMessage
+    msg shouldBe "Sample 'Something.Invalid' has an invalid name. " +
+      "Sample names must have at least 3 characters, " +
+      "must begin and end with an alphanumeric character, " +
+      "and must not have whitespace and special characters. " +
+      "Dash (-) and underscore (_) are permitted."
+
+  }
 }
 
 object MultiSampleQScriptTest {
@@ -120,6 +135,10 @@ object MultiSampleQScriptTest {
     "lib3" -> Map("test" -> "3-3")
   ))))
 
+  val sample4 = Map("samples" -> Map("Something.Invalid" -> Map("libraries" -> Map(
+    "lib1" -> Map("test" -> "4-1")
+  ))))
+
   val child = Map("samples" -> Map("child" -> Map("tags" -> Map(
     "gender" -> "male", "father" -> "father", "mother" -> "mother"))))
   val father = Map("samples" -> Map("father" -> Map("tags" -> Map("gender" -> "male"))))
@@ -136,6 +155,11 @@ object MultiSampleQScriptTest {
         .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
 
       val root = null
+
+      def getLastLogMessage: String = {
+        Logging.errors.toList.last.getMessage
+      }
+
       class Sample(id: String) extends AbstractSample(id) {
         class Library(id: String) extends AbstractLibrary(id) {
           /** Function that add library jobs */

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala

+package nl.lumc.sasc.biopet.core.report
+
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testGeneratePages(): Unit = {
+    val builder = new MultisampleReportBuilder {
+      def reportName: String = "test"
+      def indexPage: ReportPage = ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map())
+
+      def samplePage(sampleId: String, args: Map[String, Any]): ReportPage =
+        ReportPage("Libraries" -> generateLibraryPage(Map("sampleId" -> Some(sampleId))) :: Nil, Nil, Map())
+
+      def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]) = ReportPage(Nil, Nil, Map())
+    }
+
+    val tempDir = Files.createTempDir()
+    tempDir.deleteOnExit()
+    val args = Array("-s", resourcePath("/empty_summary.json"), "-o", tempDir.getAbsolutePath)
+    builder.main(args)
+    builder.extFiles.foreach(x => new File(tempDir, "ext" + File.separator + x.targetPath) should exist)
+
+    def createFile(path: String*) = new File(tempDir, path.mkString(File.separator))
+
+    createFile("index.html") should exist
+    createFile("Samples", "index.html") should exist
+    createFile("Samples", "sampleName", "index.html") should exist
+    createFile("Samples", "sampleName", "Libraries", "index.html") should exist
+    createFile("Samples", "sampleName", "Libraries", "libName", "index.html") should exist
+  }
+
+}

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala

+package nl.lumc.sasc.biopet.core.report
+
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ DataProvider, Test }
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class ReportBuilderTest extends TestNGSuite with Matchers {
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @DataProvider(name = "testGeneratePages")
+  def generatePageProvider = {
+    val sample = Array(Some("sampleName"), None)
+    val lib = Array(Some("libName"), None)
+    val nested = Array(false, true)
+    for (s <- sample; l <- lib; n <- nested) yield Array(s, l, n)
+  }
+
+  @Test(dataProvider = "testGeneratePages")
+  def testGeneratePages(sample: Option[String], lib: Option[String], nested: Boolean): Unit = {
+    val builder = new ReportBuilder {
+      def reportName: String = "test"
+      def indexPage: ReportPage = ReportPage(
+        (if (nested) "p1" -> ReportPage(Nil, Nil, Map()) :: Nil else Nil), Nil, Map())
+    }
+
+    val tempDir = Files.createTempDir()
+    tempDir.deleteOnExit()
+    val args = Array("-s", resourcePath("/empty_summary.json"), "-o", tempDir.getAbsolutePath) ++
+      sample.map(x => Array("-a", s"sampleId=$x")).getOrElse(Array()) ++
+      lib.map(x => Array("-a", s"libId=$x")).getOrElse(Array())
+    builder.main(args)
+    builder.sampleId shouldBe sample
+    builder.libId shouldBe lib
+    builder.extFiles.foreach(x => new File(tempDir, "ext" + File.separator + x.targetPath) should exist)
+    new File(tempDir, "index.html") should exist
+    new File(tempDir, "p1" + File.separator + "index.html").exists() shouldBe nested
+  }
+
+  @Test
+  def testCountPages: Unit = {
+    ReportBuilder.countPages(ReportPage(Nil, Nil, Map())) shouldBe 1
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 2
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage(Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 3
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 3
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 4
+  }
+
+  @Test
+  def testRenderTemplate: Unit = {
+    ReportBuilder.templateCache = Map()
+    ReportBuilder.templateCache shouldBe empty
+    ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "test")) shouldBe "test"
+    ReportBuilder.templateCache.size shouldBe 1
+    ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "bla")) shouldBe "bla"
+    ReportBuilder.templateCache.size shouldBe 1
+  }
+}

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala

+package nl.lumc.sasc.biopet.core.report
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class ReportSectionTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testSectionRender: Unit = {
+    ReportSection("/template.ssp", Map("arg" -> "test")).render() shouldBe "test"
+    ReportSection("/template.ssp").render(Map("arg" -> "test")) shouldBe "test"
+  }
+}

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

@@ -197,7 +197,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
 object WriteSummaryTest {
   def makeWriter(root: Configurable, c: Map[String, Any] = Map()) = new WriteSummary(root) {
-    override def globalConfig = new Config(c)
+    override def globalConfig = new Config(c + ("exe" -> "test"))
     override def outputs = Seq()
     override def inputs = Seq()
     qSettings = new QSettings {
@@ -238,7 +238,7 @@ object WriteSummaryTest {
       libId = l
       summaryName = "test"
       outputDir = new File(".").getAbsoluteFile
-      override def globalConfig = new Config(c)
+      override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
       val tempFile = File.createTempFile("summary", ".json")
@@ -256,7 +256,7 @@ object WriteSummaryTest {
     new MultiSampleQScript with QScript {
       summaryName = "test"
       outputDir = new File(".").getAbsoluteFile
-      override def globalConfig = new Config(c)
+      override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
       val tempFile = File.createTempFile("summary", ".json")

public/yamsvp/src_old/test/resources/log4j.properties → public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py

+#!/usr/bin/env python
 #
 # Biopet is built on top of GATK Queue for building bioinformatic
 # pipelines. It is mainly intended to support LUMC SHARK cluster which is running
@@ -14,12 +15,20 @@
 # license, please contact us to obtain a separate license.
 #
 
-# Set root logger level to DEBUG and its only appender to A1.
-log4j.rootLogger=ERROR, A1
 
-# A1 is set to be a ConsoleAppender.
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
+from __future__ import print_function
 
-# A1 uses PatternLayout.
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
+__author__="Peter van 't Hof"
+
+import sys
+import re
+
+upacPatern = re.compile(r'[RYKMSWBDHV]')
+
+if __name__ == "__main__":
+    for line in sys.stdin:
+        l = line.strip().split("\t")
+        if len(l) >= 3:
+            l[3] = upacPatern.sub("N", l[3])
+
+        print("\t".join(map(str, l)))

public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py

@@ -33,7 +33,9 @@ if __name__ == "__main__":
     """
     for line in sys.stdin:
         l = line.strip().split("\t")
-        if l[3] == "0":
+        l[2] = upacPatern.sub("N", l[2])
+
+        if len(l) < 4 or l[3] == "0":
             # no alignment to this position
             print("\t".join(map(str, l)))
             continue
@@ -49,5 +51,4 @@ if __name__ == "__main__":
         if new_size == 0:
             l[5] = ""
 
-        l[2] = upacPatern.sub("N", l[2])
         print("\t".join(map(str, l)))

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -114,7 +114,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var fasta: Option[String] = config("fasta")
   var sift: Option[String] = config("sift")
   var polyphen: Option[String] = config("polyphen")
-  var custom: Option[String] = config("custom")
+  var custom: List[String] = config("custom", default = Nil)
   var plugin: List[String] = config("plugin", default = Nil)
   var individual: Option[String] = config("individual")
   var fields: Option[String] = config("fields")
@@ -227,7 +227,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     optional("--fasta", fasta) +
     optional("--sift", sift) +
     optional("--polyphen", polyphen) +
-    optional("--custom", custom) +
+    repeat("--custom", custom) +
     repeat("--plugin", plugin) +
     optional("--individual", individual) +
     optional("--fields", fields) +

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala

@@ -69,8 +69,8 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Vers
     optional("--threads", nCoresRequest) +
     conditional(quick, "--quick") +
     optional("--min_hits", minHits) +
-    optional("--unclassified-out ", unclassified_out.get) +
-    optional("--classified-out ", classified_out.get) +
+    optional("--unclassified-out ", unclassified_out) +
+    optional("--classified-out ", classified_out) +
     required("--output", output) +
     conditional(preLoad, "--preload") +
     conditional(paired, "--paired") +

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

@@ -65,8 +65,10 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
 
   /** Returns command to execute */
   override def cmdLine = super.cmdLine +
-    required("INPUT=", input, spaceSeparated = false) +
-    required("OUTPUT=", output, spaceSeparated = false) +
+    (if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
+    else required("INPUT=", input, spaceSeparated = false)) +
+    (if (outputAsStsout) required("OUTPUT=", new File("/dev/stdout"), spaceSeparated = false)
+    else required("OUTPUT=", output, spaceSeparated = false)) +
     required("SORT_ORDER=", sortOrder, spaceSeparated = false) +
     required("RGID=", RGID, spaceSeparated = false) +
     required("RGLB=", RGLB, spaceSeparated = false) +

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala

@@ -34,6 +34,9 @@ class ReorderSam(val root: Configurable) extends Picard with Reference {
   @Output(doc = "Output SAM or BAM file", required = true)
   var output: File = null
 
+  @Output(doc = "The output file to bam file to", required = true)
+  lazy val outputIndex: File = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+
   @Argument(doc = "Allow incomplete dict concordance", required = false)
   var allowIncompleteDictConcordance: Boolean = config("allow_incomplete_dict_concordance", default = false)
 
@@ -49,6 +52,8 @@ class ReorderSam(val root: Configurable) extends Picard with Reference {
     conditional(allowIncompleteDictConcordance, "ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE") +
     conditional(allowContigLengthDiscordance, "ALLOW_CONTIG_LENGTH_DISCORDANCE=TRUE") +
     required("REFERENCE=", reference, spaceSeparated = false) +
-    required("INPUT=", input, spaceSeparated = false) +
-    required("OUTPUT=", output, spaceSeparated = false)
+    (if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
+    else required("INPUT=", input, spaceSeparated = false)) +
+    (if (outputAsStsout) required("OUTPUT=", new File("/dev/stdout"), spaceSeparated = false)
+    else required("OUTPUT=", output, spaceSeparated = false))
 }