Merge with develop

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala

@@ -47,4 +47,26 @@ object IoUtils {
       }
     }
   }
+
+  /** Possible compression extensions to trim from input files. */
+  val zipExtensions = Set(".gz", ".gzip", ".bzip2", ".bz", ".xz", ".zip")
+
+  /**
+   * Given a file object and a set of compression extensions, return the filename without any of the compression
+   * extensions.
+   *
+   * Examples:
+   *  - my_file.fq.gz returns "my_file.fq"
+   *  - my_other_file.fastq returns "my_file.fastq"
+   *
+   * @param f Input file object.
+   * @param exts Possible compression extensions to trim.
+   * @return Filename without compression extension.
+   */
+  def getUncompressedFileName(f: File, exts: Set[String] = zipExtensions): String =
+    exts.foldLeft(f.getName) {
+      (fname, ext) =>
+        if (fname.toLowerCase.endsWith(ext)) fname.dropRight(ext.length)
+        else fname
+    }
 }

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

@@ -19,7 +19,9 @@ 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.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.IoUtils._
 import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+
 import org.broadinstitute.gatk.queue.QScript
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -53,8 +55,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
 
   var paired: Boolean = input_R2.isDefined
-  var R1_ext: String = _
-  var R2_ext: String = _
   var R1_name: String = _
   var R2_name: String = _
 
@@ -85,21 +85,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     inputFiles :+= new InputFile(input_R1)
     input_R2.foreach(inputFiles :+= new InputFile(_))
 
-    if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
-    else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
-    else R1_name = input_R1.getName
-    R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.length)
-    R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
-
-    input_R2 match {
-      case Some(fileR2) =>
-        paired = true
-        if (fileR2.endsWith(".gz")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gz"))
-        else if (fileR2.endsWith(".gzip")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gzip"))
-        else R2_name = fileR2.getName
-        R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.length)
-        R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
-      case _ =>
+    R1_name = getUncompressedFileName(input_R1)
+    input_R2.foreach { fileR2 =>
+      paired = true
+      R2_name = getUncompressedFileName(fileR2)
     }
   }
 
@@ -214,6 +203,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
           qcCmdR2.beforeCmd()
           fqSync.beforeCmd()
           commands = qcCmdR1.jobs ::: qcCmdR2.jobs ::: fqSync :: Nil
+          commands.foreach(addPipeJob)
           super.beforeCmd()
         }
       }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction, BiopetPipe }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
 import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -73,18 +73,20 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
       case _ => None
     }
     if (seqtk.Q.isDefined) seqtk.V = true
+    addPipeJob(seqtk)
 
     clip = if (!flexiprep.skipClip) {
       val foundAdapters = fastqc.foundAdapters.map(_.seq)
       if (foundAdapters.nonEmpty) {
-        val cutadept = new Cutadapt(root)
-        cutadept.fastq_input = seqtk.output
-        cutadept.fastq_output = new File(output.getParentFile, input.getName + ".cutadept.fq")
-        cutadept.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
-        if (cutadept.default_clip_mode == "3") cutadept.opt_adapter ++= foundAdapters
-        else if (cutadept.default_clip_mode == "5") cutadept.opt_front ++= foundAdapters
-        else if (cutadept.default_clip_mode == "both") cutadept.opt_anywhere ++= foundAdapters
-        Some(cutadept)
+        val cutadapt = new Cutadapt(root)
+        cutadapt.fastq_input = seqtk.output
+        cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
+        cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
+        if (cutadapt.default_clip_mode == "3") cutadapt.opt_adapter ++= foundAdapters
+        else if (cutadapt.default_clip_mode == "5") cutadapt.opt_front ++= foundAdapters
+        else if (cutadapt.default_clip_mode == "both") cutadapt.opt_anywhere ++= foundAdapters
+        addPipeJob(cutadapt)
+        Some(cutadapt)
       } else None
     } else None
 
@@ -92,17 +94,18 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
       val sickle = new Sickle(root)
       sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
       sickle.input_R1 = clip match {
-        case Some(clip) => clip.fastq_output
-        case _          => seqtk.output
+        case Some(c) => c.fastq_output
+        case _       => seqtk.output
       }
       sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
+      addPipeJob(sickle)
       Some(sickle)
     } else None
 
     val outputFile = (clip, trim) match {
-      case (_, Some(trim)) => trim.output_R1
-      case (Some(clip), _) => clip.fastq_output
-      case _               => seqtk.output
+      case (_, Some(t)) => t.output_R1
+      case (Some(c), _) => c.fastq_output
+      case _            => seqtk.output
     }
 
     if (compress) outputCommand = {
@@ -131,10 +134,10 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
   def cmdLine = {
 
     val cmd = (clip, trim) match {
-      case (Some(clip), Some(trim)) => new BiopetFifoPipe(root, seqtk :: clip :: trim :: outputCommand :: Nil)
-      case (Some(clip), _)          => new BiopetFifoPipe(root, seqtk :: clip :: outputCommand :: Nil)
-      case (_, Some(trim))          => new BiopetFifoPipe(root, seqtk :: trim :: outputCommand :: Nil)
-      case _                        => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
+      case (Some(c), Some(t)) => new BiopetFifoPipe(root, seqtk :: c :: t :: outputCommand :: Nil)
+      case (Some(c), _)       => new BiopetFifoPipe(root, seqtk :: c :: outputCommand :: Nil)
+      case (_, Some(t))       => new BiopetFifoPipe(root, seqtk :: t :: outputCommand :: Nil)
+      case _                  => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
     }
 
     //val cmds = (Some(seqtk) :: clip :: trim :: Some(new Gzip(root)) :: Nil).flatten