Merge branch 'develop' into fix-vcfstats-summary

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

@@ -155,7 +155,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     super.beforeGraph()
     if (!cache && !database) {
       Logging.addError("Must either set 'cache' or 'database' to true for VariantEffectPredictor")
-    } else if (cache && dir.isEmpty) {
+    } else if (cache && dir.isEmpty && dirCache.isEmpty) {
       Logging.addError("Must supply 'dir_cache' to cache for VariantEffectPredictor")
     }
     if (statsText) _summary = new File(output.getAbsolutePath + "_summary.txt")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala

@@ -58,6 +58,8 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
   @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
   var log_to_file: File = _
 
+  override def defaultCoreMemory = 4.0
+
   override def beforeGraph() = {
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()

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

@@ -36,7 +36,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFunction with Summariza
   @Output(doc = "Output JSON", shortName = "output", required = true)
   var output: File = null
 
-  override def defaultCoreMemory = 2.5
+  override def defaultCoreMemory = 4.0
 
   override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
 

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

@@ -29,6 +29,8 @@ class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
   @Input(doc = "Input R1 fastq file", required = false)
   var r2Fastq: Option[File] = None
 
+  override def defaultCoreMemory = 4.0
+
   override def cmdLine = super.cmdLine +
     required("-i", r1Fastq) +
     optional("-j", r2Fastq)

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

@@ -43,7 +43,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFunction with Refere
 
   var fields: List[(String, String, Option[String])] = List()
 
-  override def defaultCoreMemory = 2.0
+  override def defaultCoreMemory = 4.0
 
   override def beforeGraph() {
     super.beforeGraph()

docs/pipelines/tinycap.md

@@ -55,35 +55,23 @@ One can specify other options such as: `bowtie` (alignment) options, clipping an
   "chunkmbs": 256,  # this is a performance option, keep it high (256) as many alternative alignments are possible
   "seedmms": 3,
   "seedlen": 25,
-  "k": 5,           # take and report best 5 alignments 
-  "best": true      # sort by best hit
+  "k": 3,           # take and report best 3 alignments 
+  "best": true,     # sort by best hit,
+  "strata" true     # select from best strata
 },
 "sickle": {
-  "lengthThreshold": 8  # minimum length to keep after trimming
+  "lengthThreshold": 15  # minimum length to keep after trimming
 },
 "cutadapt": {
-  "error_rate": 0.2,    # recommended: 0.2, allow more mismatches in adapter to be clipped of (ratio)
-  "minimum_length":  8, # minimum length to keep after clipping, setting lower will cause multiple alignments afterwards
+  "error_rate": 0.1,    # recommended: 0.1, allow more mismatches in adapter to be clipped of (ratio)
+  "minimum_length":  15, # minimum length to keep after clipping, setting lower will cause multiple alignments afterwards
   "q": 30,              # minimum quality over the read after the clipping in order to keep and report the read
-  "default_clip_mode": "both",  # clip from: front/end/both (5'/3'/both). Depending on the protocol. Setting `both` makes clipping take more time, but is safest to do on short sequences such as smallRNA.
-  "times": 2            # in cases of chimera reads/adapters, how many times should cutadapt try to remove am adapter-sequence
+  "default_clip_mode": "3",  # clip from: front/end/both (5'/3'/both). Depending on the protocol.
+  "times": 1,            # in cases of chimera reads/adapters, how many times should cutadapt try to remove am adapter-sequence
+  "ignore_fastqc_adapters": true    # by default ignore the detected adapters by FastQC. These tend to give false positive hits for smallRNA projects.
 }
 ```
 
-The settings above is quite strict and aggressive on the clipping with `cutadapt`. By default the option `sensitiveAdapterSearch` is turned on in the TinyCap pipeline:
-
-```json
-"fastqc": {
-    "sensitiveAdapterSearch": true
-}
-```
-
-This setting is turned on to enable aggressive adapter trimming. e.g. found (partial) adapters in `FastQC` 
-are all used in `Cutadapt`. Depending on the sequencing technique and sample preparation, e.g. short 
-sequences (76bp - 100bp). Turning of this option will still produce sensible results.
-
-
-
 ## Examine results
 
 ### Result files

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -19,6 +19,10 @@
     val trimCount = summary.getLibraryValues("flexiprep", "settings", "skip_trim").count(_._2 == Some(false))
     val clipCount = summary.getLibraryValues("flexiprep", "settings", "skip_clip").count(_._2 == Some(false))
     val librariesCount = summary.samples.foldLeft(0)(_ + summary.libraries(_).size)
+
+    val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
+    summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "settings", "paired").get.asInstanceOf[Boolean]
+    else summary.getLibraryValues("flexiprep", "settings", "paired").values.exists(_ == Some(true))
 }#
 
 #if (showIntro)
@@ -62,9 +66,6 @@
 
 #if (showPlot)
     #{
-        val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
-            summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "settings", "paired").get.asInstanceOf[Boolean]
-        else summary.getLibraryValues("flexiprep", "settings", "paired").values.exists(_ == Some(true))
         FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
         if (paired) FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
     }#
@@ -105,6 +106,7 @@
         <th>Before QC</th>
         <th>Clipping</th>
         <th>Trimming</th>
+        #if (paired == true) <th>Out of Sync</th> #end
         <th>After QC</th>
     </tr></thead>
     <tbody>
@@ -140,8 +142,8 @@
                     #for (read <- reads)
                         #if (read == "R2") </tr><tr> #end
                         #{
-                            val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
-                            val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total")
+                            val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total").getOrElse(0).toString.toLong
+                            val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total").getOrElse(0).toString.toLong
                             val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).toString.toLong
                             val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).toString.toLong
                             var trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_total").getOrElse(0).toString.toLong
@@ -150,6 +152,7 @@
                         <td>${beforeTotal}</td>
                         <td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
                         <td>${trimmingDiscarded}</td>
+                        #if (paired == true) <td>${beforeTotal - clippingDiscardedToShort - clippingDiscardedToLong - trimmingDiscarded - afterTotal}</td> #end
                         <td>${afterTotal}</td>
                     #end
                 </tr>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.IoUtils._
-import nl.lumc.sasc.biopet.extensions.tools.{ ValidateFastq, SeqStat, FastqSync }
-
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat, ValidateFastq }
+import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.queue.QScript
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -74,33 +74,37 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
   /** Function that's need to be executed before the script is accessed */
   def init() {
-    require(outputDir != null, "Missing output directory on flexiprep module")
-    require(inputR1 != null, "Missing input R1 on flexiprep module")
-    require(sampleId != null, "Missing sample ID on flexiprep module")
-    require(libId != null, "Missing library ID on flexiprep module")
+    if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
+    if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on flexiprep module")
+    if (libId == null || libId == None) Logging.addError("Missing library ID on flexiprep module")
 
-    paired = inputR2.isDefined
+    if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
+    else {
+      paired = inputR2.isDefined
 
-    inputFiles :+= new InputFile(inputR1)
-    inputR2.foreach(inputFiles :+= new InputFile(_))
+      inputFiles :+= new InputFile(inputR1)
+      inputR2.foreach(inputFiles :+= new InputFile(_))
 
-    R1Name = getUncompressedFileName(inputR1)
-    inputR2.foreach { fileR2 =>
-      paired = true
-      R2Name = getUncompressedFileName(fileR2)
+      R1Name = getUncompressedFileName(inputR1)
+      inputR2.foreach { fileR2 =>
+        paired = true
+        R2Name = getUncompressedFileName(fileR2)
+      }
     }
   }
 
   /** Script to add jobs */
   def biopetScript() {
-    runInitialJobs()
+    if (inputR1 != null) {
+      runInitialJobs()
 
-    if (paired) runTrimClip(inputR1, inputR2, outputDir)
-    else runTrimClip(inputR1, outputDir)
+      if (paired) runTrimClip(inputR1, inputR2, outputDir)
+      else runTrimClip(inputR1, outputDir)
 
-    val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
-    val R2Files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
-    runFinalize(R1Files.toList, R2Files.toList)
+      val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
+      val R2Files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
+      runFinalize(R1Files.toList, R2Files.toList)
+    }
   }
 
   /** Add init non chunkable jobs */

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.tools.{ ValidateFastq, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, ValidateFastq }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
@@ -83,6 +83,18 @@ class FlexiprepTest extends TestNGSuite with Matchers {
 
   }
 
+  @Test
+  def testNoSample: Unit = {
+    val map = ConfigUtils.mergeMaps(Map(
+      "output_dir" -> FlexiprepTest.outputDir
+    ), Map(FlexiprepTest.executables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    intercept[IllegalStateException] {
+      flexiprep.script()
+    }
+  }
+
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
     FileUtils.deleteDirectory(FlexiprepTest.outputDir)

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

@@ -18,6 +18,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -48,6 +49,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   def init(): Unit = {
     require(fastqR1.isDefined || bamFile.isDefined, "Please specify fastq-file(s) or bam file")
     require(fastqR1.isDefined != bamFile.isDefined, "Provide either a bam file or a R1/R2 file")
+    if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
 
     if (outputName == null) {
       if (fastqR1.isDefined) outputName = fastqR1.map(_.getName
@@ -80,6 +82,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
       val flexiprep = new Flexiprep(this)
       flexiprep.inputR1 = r1
       flexiprep.inputR2 = r2
+      flexiprep.sampleId = if (sampleId.isEmpty) Some("noSampleName") else sampleId
+      flexiprep.libId = if (libId.isEmpty) Some("noLibName") else libId
       flexiprep.outputDir = new File(outputDir, "flexiprep")
       add(flexiprep)
       (flexiprep.fastqR1Qc, flexiprep.fastqR2Qc)

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

@@ -80,6 +80,8 @@ class GearsSingleTest extends TestNGSuite with Matchers {
     ), Map(GearsSingleTest.executables.toSeq: _*))
 
     val gears: GearsSingle = initPipeline(map)
+    gears.sampleId = Some("sampleName")
+    gears.libId = Some("libName")
 
     if (fromBam) {
       gears.bamFile = Some(GearsSingleTest.bam)
@@ -113,6 +115,18 @@ class GearsSingleTest extends TestNGSuite with Matchers {
     gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken) 1 else 0)
   }
 
+  @Test
+  def testNoSample: Unit = {
+    val map = ConfigUtils.mergeMaps(Map(
+      "output_dir" -> GearsSingleTest.outputDir
+    ), Map(GearsSingleTest.executables.toSeq: _*))
+    val gears: GearsSingle = initPipeline(map)
+
+    intercept[IllegalArgumentException] {
+      gears.script()
+    }
+  }
+
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
     FileUtils.deleteDirectory(GearsSingleTest.outputDir)

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -117,6 +117,7 @@ class Gentrap(val root: Configurable) extends QScript
     ),
     // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
     "mapping" -> Map(
+      "aligner" -> "gsnap",
       "skip_markduplicates" -> true
     )
   )

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala

@@ -16,6 +16,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.measures
 
 import nl.lumc.sasc.biopet.core.annotations.AnnotationGtf
 import nl.lumc.sasc.biopet.extensions.HtseqCount
+import nl.lumc.sasc.biopet.extensions.picard.SortSam
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -25,19 +26,31 @@ import org.broadinstitute.gatk.queue.QScript
 class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
   def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, numHeaderLines = 0, fallback = "0")
 
-  override def fixedValues: Map[String, Any] = Map("htseqcount" -> Map("order" -> "pos"))
+  override def fixedValues: Map[String, Any] = Map("htseqcount" -> Map("order" -> ""))
+
+  lazy val sortOnId: Boolean = config("sort_on_id", default = true)
 
   /** Pipeline itself */
   def biopetScript(): Unit = {
     val jobs = bamFiles.map {
       case (id, file) =>
-        //TODO: ID sorting job
+
+        val bamFile = if (sortOnId) {
+          val sortSam = new SortSam(this)
+          sortSam.input = file
+          sortSam.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
+          sortSam.sortOrder = "queryname"
+          sortSam.isIntermediate = true
+          add(sortSam)
+          sortSam.output
+        } else file
 
         val job = new HtseqCount(this)
         job.inputAnnotation = annotationGtf
-        job.inputAlignment = file
+        job.inputAlignment = bamFile
         job.output = new File(outputDir, s"$id.$name.counts")
         job.format = Option("bam")
+        job.order = if (sortOnId) Some("name") else Some("pos")
         add(job)
         id -> job
     }

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

@@ -17,7 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.gentrap
 import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
 import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
+import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
 import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
@@ -26,7 +29,7 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.{ DataProvider, Test }
 
-abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNGSuite with Matchers {
+abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: Option[String]) extends TestNGSuite with Matchers {
 
   def initPipeline(map: Map[String, Any]): Gentrap = {
     new Gentrap() {
@@ -105,15 +108,18 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
     val settings = Map(
       "output_dir" -> GentrapTest.outputDir,
       "gsnap" -> Map("db" -> "test", "dir" -> "test"),
-      "aligner" -> "gsnap",
       "expression_measures" -> expMeasures,
       "strand_protocol" -> strandProtocol
-    )
+    ) ++ aligner.map("aligner" -> _)
     val config = ConfigUtils.mergeMaps(settings ++ sampleConfig, Map(GentrapTest.executables.toSeq: _*))
     val gentrap: Gentrap = initPipeline(config)
 
     gentrap.script()
-    val functions = gentrap.functions.groupBy(_.getClass)
+    val functions = gentrap.functions.flatMap {
+      case f: BiopetFifoPipe => f.pipesJobs
+      case f: BiopetPipe     => f.pipesJobs
+      case f                 => List(f)
+    }.groupBy(_.getClass)
     val numSamples = sampleConfig("samples").size
 
     if (expMeasures.contains("fragments_per_gene"))
@@ -139,16 +145,29 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
       assert(gentrap.functions.exists(_.isInstanceOf[Cufflinks]))
       assert(gentrap.functions.exists(_.isInstanceOf[Ln]))
     }
+
+    val classMap = Map(
+      "gsnap" -> classOf[Gsnap],
+      "tophat" -> classOf[Tophat],
+      "star" -> classOf[Star],
+      "star-2pass" -> classOf[Star],
+      "hisat2" -> classOf[Hisat2]
+    )
+
+    val alignerClass = classMap.get(aligner.getOrElse("gsnap"))
+
+    alignerClass.foreach(c => assert(functions.keys.exists(_ == c)))
+    classMap.values.filterNot(Some(_) == alignerClass).foreach(x => assert(!functions.keys.exists(_ == x)))
   }
 
 }
 
-class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene")
-//class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon")
-class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts")
-class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict")
-class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided")
-class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind")
+class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene", None)
+//class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon", None)
+class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts", None)
+class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict", None)
+class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided", None)
+class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind", None)
 
 object GentrapTest {
   val outputDir = Files.createTempDir()

tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala

@@ -64,22 +64,24 @@ class TinyCap(val root: Configurable) extends QScript
     "bowtie" -> Map(
       "chunkmbs" -> 256,
       "seedmms" -> 3,
-      "seedlen" -> 25,
-      "k" -> 5,
-      "best" -> true
+      "seedlen" -> 28,
+      "k" -> 3,
+      "best" -> true,
+      "strata" -> true
     ),
     "sickle" -> Map(
       "lengthThreshold" -> 15
     ),
     "fastqc" -> Map(
-      "sensitiveAdapterSearch" -> true
+      "sensitiveAdapterSearch" -> false
     ),
     "cutadapt" -> Map(
-      "error_rate" -> 0.2,
+      "error_rate" -> 0.1,
       "minimum_length" -> 15,
       "q" -> 30,
-      "default_clip_mode" -> "both",
-      "times" -> 2
+      "default_clip_mode" -> "3",
+      "times" -> 1,
+      "ignore_fastqc_adapters" -> true
     )
   )