Add bowtie2 to Mapping (and add wrapper for bowtie2)

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+/**
+  * Extension for bowtie 2
+  *
+  * Based on version 2.2.6
+  */
+class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+  @Input(doc = "Fastq file R1", shortName = "R1")
+  var R1: File = null
+
+  @Input(doc = "Fastq file R2", shortName = "R2", required = false)
+  var R2: Option[File] = None
+
+  @Output(doc = "Output file SAM", shortName = "output", required = true)
+  var output: File = null
+
+  executable = config("exe", default = "bowtie2", freeVar = false)
+  def versionRegex = """.*[Vv]ersion:? (.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = executable + " --version"
+
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 4
+
+  /* Required */
+  var bowtieIndex: String = config("bowtie_index")
+
+  /* Input options */
+  var q: Boolean = config("q", default=true)
+  var qseq: Boolean = config("qseq", default=false)
+  var f: Boolean = config("f", default=false)
+  var r: Boolean = config("r", default=false)
+  var c: Boolean = config("c", default=false)
+  var skip: Option[Int] = config("skip")
+  var upto: Option[Int] = config("upto")
+  var trim5: Option[Int] = config("trim5")
+  var trim3: Option[Int] = config("trim3")
+  var phred33: Boolean = config("phred33")
+  var phred64: Boolean = config("phred64")
+  var int_quals: Boolean = config("int_quals")
+
+  /* Alignment options */
+  var N: Option[Int] = config("N")
+  var L: Option[Int] = config("L")
+  var i: Option[String] = config("i")
+  var n_ceil: Option[String] = config("n_ceil")
+  var dpad: Option[Int] = config("dpad")
+  var gbar: Option[Int] = config("gbar")
+  var ignore_quals: Boolean = config("ignore_quals")
+  var nofw: Boolean = config("nofw")
+  var norc: Boolean = config("norc")
+  var no_1mm_upfront: Boolean = config("no_1mm_upfront")
+  var end_to_end: Boolean = config("end_to_end")
+  var local: Boolean = config("local")
+
+  /* Scoring */
+  var ma: Option[Int] = config("ma")
+  var mp: Option[Int] = config("mp")
+  var np: Option[Int] = config("np")
+  var rdg: Option[String] = config("rdg")
+  var rfg: Option[String] = config("rfg")
+  var score_min: Option[String] = config("score_min")
+
+  /* Reporting */
+  var k: Option[Int] = config("k")
+  var all: Option[Int] = config("all")
+
+  /* Effort */
+  var D: Option[Int] = config("D")
+  var R: Option[Int] = config("R")
+
+  /* Paired-end */
+  var minins: Option[Int] = config("minins")
+  var maxins: Option[Int] = config("maxins")
+  var fr: Boolean = config("fr")
+  var rf: Boolean = config("rf")
+  var ff: Boolean = config("ff")
+  var no_mixed: Boolean = config("no_mixed")
+  var no_discordant: Boolean = config("no_discordant")
+  var no_dovetail: Boolean = config("no_dovetail")
+  var no_contain: Boolean = config("no_contain")
+  var no_overlap: Boolean = config("no_overlap")
+
+  /* Output */
+  var time: Boolean = config("no_overlap")
+
+  var un: Option[String] = config("un")
+  var al: Option[String] = config("al")
+  var un_conc: Option[String] = config("un_conc")
+  var al_conc: Option[String] = config("al_conc")
+
+  var un_gz: Option[String] = config("un_gz")
+  var al_gz: Option[String] = config("al_gz")
+  var un_conc_gz: Option[String] = config("un_conc_gz")
+  var al_conc_gz: Option[String] = config("al_conc_gz")
+
+  var un_bz2: Option[String] = config("un_bz2")
+  var al_bz2: Option[String] = config("al_bz2")
+  var un_conc_bz2: Option[String] = config("un_conc_bz2")
+  var al_conc_bz2: Option[String] = config("al_conc_bz2")
+
+  var quiet: Boolean = config("quiet")
+  var met_file: Option[String] = config("met_file")
+  var met_stderr: Boolean = config("met_stderr")
+  var met: Option[Int] = config("met")
+
+  var no_unal: Boolean = config("no_unal")
+  var no_head: Boolean = config("no_head")
+  var no_sq: Boolean = config("no_sq")
+
+  var rg_id: Option[String] = config("rg_id")
+  var rg: Option[String] = config("rg")
+
+  var omit_sec_seq: Boolean = config("omit_sec_seq")
+
+  /* Performance */
+  var reorder: Boolean = config("reorder")
+  var mm: Boolean = config("mm")
+
+  /* Other */
+  var qc_filter: Boolean = config("qc_filter")
+  var seed: Option[Int] = config("seed")
+  var non_deterministic: Boolean = config("non_deterministic")
+
+  /** return commandline to execute */
+  def cmdLine = required(executable) +
+    conditional(q, "-q") +
+    conditional(qseq, "--qseq") +
+    conditional(f, "-f") +
+    conditional(r, "-r") +
+    conditional(c, "-c") +
+    optional("--skip", skip) +
+    optional("--upto", upto) +
+    optional("--trim3", trim3) +
+    optional("--trim5", trim5) +
+    conditional(phred33, "--phred33") +
+    conditional(phred64, "--phred64") +
+    conditional(int_quals, "--int-quals") +
+    /* Alignment options */
+    optional("-N", N) +
+    optional("-L", L) +
+    optional("-i", i) +
+    optional("--n-ceil", n_ceil) +
+    optional("--dpad", dpad) +
+    optional("--gbar", gbar) +
+    optional("--ignore-quals", ignore_quals) +
+    conditional(nofw, "--nofw") +
+    conditional(norc, "--norc") +
+    conditional(no_1mm_upfront, "--no-1mm-upfront") +
+    conditional(end_to_end, "--end-to-end") +
+    conditional(local, "--local") +
+    /* Scoring */
+    optional("--ma", ma) +
+    optional("--mp", mp) +
+    optional("--np", np) +
+    optional("--rdg", rdg) +
+    optional("--rfg", rfg) +
+    optional("--score-min", score_min) +
+    /* Reporting */
+    optional("-k", k) +
+    optional("--all", all) +
+    /* Effort */
+    optional("-D", D) +
+    optional("-R", R) +
+    /* Paired End */
+    optional("-minins", minins) +
+    optional("-maxins", maxins) +
+    conditional(fr, "--fr") +
+    conditional(rf, "--rf") +
+    conditional(ff, "--ff") +
+    conditional(no_mixed, "--no-mixed") +
+    conditional(no_discordant, "--no-discordant") +
+    conditional(no_dovetail, "--no-dovetail") +
+    conditional(no_contain, "--no-contain") +
+    conditional(no_overlap, "--no-overlap") +
+    /* Output */
+    conditional(time, "--time") +
+    optional("--un", un) +
+    optional("--al", al) +
+    optional("--un-conc", un_conc) +
+    optional("--al-conc", al_conc) +
+    optional("--un-gz", un_gz) +
+    optional("--al-gz", al_gz) +
+    optional("--un-conc-gz", un_conc_gz) +
+    optional("--al-conc-gz", al_conc_gz) +
+    optional("--un-bz2", un_bz2) +
+    optional("--al-bz2", al_bz2) +
+    optional("--un-conc-bz2", un_conc_bz2) +
+    optional("--al-conc-bz2", al_conc_bz2) +
+    conditional(quiet, "--quiet") +
+    optional("--met-file", met_file) +
+    conditional(met_stderr, "--met-stderr") +
+    optional("--met", met) +
+    conditional(no_unal, "--no-unal") +
+    conditional(no_head, "--no-head") +
+    conditional(no_sq, "--no-sq") +
+    optional("--rg-id", rg_id) +
+    optional("--rg", rg) +
+    conditional(omit_sec_seq, "--omit-sec-seq") +
+    /* Performance */
+    optional("--threads", threads) +
+    optional("--reorder", reorder) +
+    optional("--mm", mm) +
+    /* Other */
+    conditional(qc_filter, "--qc-filter") +
+    optional("--seed", seed) +
+    conditional(non_deterministic, "--non-deterministic") +
+    /* Required */
+    required("-x", bowtieIndex) +
+    (R2 match {
+      case Some(r2) =>
+        required("-1", R1) +
+          optional("-2", r2)
+      case _ => required("-U", R1)
+    }) +
+    (if (outputAsStsout) "" else required("-S", output))
+}

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
 import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
-import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat, _ }
+import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
@@ -219,6 +219,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
         case "bwa-mem"    => addBwaMem(R1, R2, outputBam)
         case "bwa-aln"    => addBwaAln(R1, R2, outputBam)
         case "bowtie"     => addBowtie(R1, R2, outputBam)
+        case "bowtie2"     => addBowtie2(R1, R2, outputBam)
         case "gsnap"      => addGsnap(R1, R2, outputBam)
         // TODO: make TopHat here accept multiple input files
         case "tophat"     => addTophat(R1, R2, outputBam)
@@ -437,6 +438,20 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     ar._2
   }
 
+  /** Add bowtie2 jobs **/
+  def addBowtie2(R1: File, R2: Option[File], output: File): File = {
+    val bowtie2 = new Bowtie2(this)
+    bowtie2.R1 = R1
+    if (paired) bowtie2.R2 = Some(R2.get)
+    val sortSam = new SortSam(this)
+    sortSam.output = output
+    val pipe = bowtie2 | sortSam
+    pipe.isIntermediate = chunking || !skipMarkduplicates
+    pipe.threadsCorrection = -1
+    add(pipe)
+    output
+  }
+
   /** Adds Star jobs */
   def addStar(R1: File, R2: Option[File], output: File): File = {
     val zcatR1 = extractIfNeeded(R1, output.getParentFile)

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -98,6 +98,7 @@ class MappingBwaAlnTest extends AbstractTestMapping("bwa-aln")
 class MappingStarTest extends AbstractTestMapping("star")
 class MappingStar2PassTest extends AbstractTestMapping("star-2pass")
 class MappingBowtieTest extends AbstractTestMapping("bowtie")
+class MappingBowtie2Test extends AbstractTestMapping("bowtie2")
 class MappingStampyTest extends AbstractTestMapping("stampy")
 class MappingGsnapTest extends AbstractTestMapping("gsnap")
 class MappingTophatTest extends AbstractTestMapping("tophat")
@@ -142,6 +143,7 @@ object MappingTest {
     "bwa" -> Map("exe" -> "test"),
     "star" -> Map("exe" -> "test"),
     "bowtie" -> Map("exe" -> "test"),
+    "bowtie2" -> Map("exe" -> "test"),
     "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test")