Add initial hisat2 wrapper

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.hisat
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Extension for hisat2
+ *
+ * Based on version 2.0.4
+ */
+class Hisat2(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+
+  // TODO: handle --sra-acc flag. This is currently unsupported by the wrapper.
+
+  @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 = "hisat2", freeVar = false)
+  def versionRegex = """.*hisat2-align-s version (.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = executable + " --version"
+
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 4
+
+  /* Required */
+  var hisat2Index: String = config("hisat2_index")
+
+  /* Input options */
+  var q: Boolean = config("q", default = false)
+  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", default = false)
+  var phred64: Boolean = config("phred64", default = false)
+  var intQuals: Boolean = config("int_quals", default = false)
+
+  /* Alignment options */
+  var nCeil: Option[String] = config("n_ceil")
+  var ignoreQuals: Boolean = config("ignore_quals", default = false)
+  var nofw: Boolean = config("nofw", default = false)
+  var norc: Boolean = config("norc", default = false)
+
+  /* Spliced alignment */
+  var penCansplice: Option[Int] = config("pen_cansplice")
+  var penNoncansplice: Option[Int] = config("pen_noncansplice")
+  var penCanintronlen: Option[Int] = config("pen_canintronlen")
+  var penNoncanintronlen: Option[Int] = config("pen_noncanintronlen")
+  var minIntronlen: Option[Int] = config("min_intronlen")
+  var maxIntronlen: Option[Int] = config("max_intronlen")
+  var knownSplicesiteInfile: Option[File] = config("known_splicesite_infile")
+  var novelSplicesiteOutfile: Option[File] = config("novel_splicesite_outfile")
+  var novelSplicesiteInfile: Option[File] = config("novel_splicesite_infile")
+  var noTempSplicesite: Boolean = config("no_temp_splicesite", default = false)
+  var noSplicedAlignment: Boolean = config("no_spliced_alignment", default = false)
+  var rnaStrandness: Option[String] = config("rna_strandness")
+  var tmo: Boolean = config("tmo", default = false)
+  var dta: Boolean = config("dta", default = false)
+  var dtaCufflinks: Boolean = config("dta_cufflinks", default = false)
+
+  /* Scoring */
+  var ma: Option[Int] = config("ma")
+  var mp: Option[String] = config("mp")  // TODO: should be (Int, Int)
+  var sp: Option[String] = config("sp")  // TODO: should be (Int, Int)
+  var np: Option[Int] = config("np")
+  var rdg: Option[String] = config("rdg")  // TODO: should be (Int, Int)
+  var rfg: Option[String] = config("rfg")  // TODO: should be (Int, Int)
+  var scoreMin: Option[String] = config("score_min")
+
+  /* Reporting */
+  var k: Option[Int] = config("k")
+  var all: Option[Int] = config("all")
+
+  /* Paired-end */
+  var fr: Boolean = config("fr", default = false)
+  var rf: Boolean = config("rf", default = false)
+  var ff: Boolean = config("ff", default = false)
+  var noMixed: Boolean = config("no_mixed", default = false)
+  var noDiscordant: Boolean = config("no_discordant", default = false)
+
+  /* Output */
+  var time: Boolean = config("no_overlap", default = false)
+
+  var un: Option[String] = config("un")
+  var al: Option[String] = config("al")
+  var unConc: Option[String] = config("un_conc")
+  var alConc: Option[String] = config("al_conc")
+
+  var unGz: Option[String] = config("un_gz")
+  var alGz: Option[String] = config("al_gz")
+  var unConcGz: Option[String] = config("un_conc_gz")
+  var alConcGz: Option[String] = config("al_conc_gz")
+
+  var unBz2: Option[String] = config("un_bz2")
+  var alBz2: Option[String] = config("al_bz2")
+  var unConcBz2: Option[String] = config("un_conc_bz2")
+  var alConcBz2: Option[String] = config("al_conc_bz2")
+
+  var quiet: Boolean = config("quiet", default = false)
+  var metFile: Option[String] = config("met_file")
+  var metStderr: Boolean = config("met_stderr", default = false)
+  var met: Option[Int] = config("met")
+
+  var noHead: Boolean = config("no_head", default = false)
+  var noSq: Boolean = config("no_sq", default = false)
+
+  var rgId: Option[String] = config("rg_id")
+  var rg: List[String] = config("rg", default = Nil)
+
+  var omitSecSeq: Boolean = config("omit_sec_seq", default = false)
+
+  /* Performance */
+  var offrate: Option[Int] = config("offrate")
+  var reorder: Boolean = config("reorder", default = false)
+  var mm: Boolean = config("mm", default = false)
+
+  /* Other */
+  var qcFilter: Boolean = config("qc_filter", default = false)
+  var seed: Option[Int] = config("seed")
+  var nonDeterministic: Boolean = config("non_deterministic", default = false)
+  var removeChrName: Boolean = config("remove_chrname", default = false)
+  var addChrName: Boolean = config("add_chrname", default = false)
+
+  override def beforeGraph() {
+    super.beforeGraph()
+    val indexDir = new File(hisat2Index).getParentFile
+    val basename = hisat2Index.stripPrefix(indexDir.getPath + File.separator)
+    if (indexDir.exists()) {
+      if (!indexDir.list()
+        .toList
+        .filter(_.startsWith(basename))
+        .exists({ p =>
+          p.endsWith(".bt2") || p.endsWith(".bt2l")
+        }))
+        Logging.addError(s"No index files found for hisat2 in: $indexDir with basename: $basename")
+    }
+  }
+
+  /** 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(intQuals, "--int-quals") +
+    /* Alignment options */
+    optional("--n-ceil", nCeil) +
+    conditional(ignoreQuals, "--ignore-quals") +
+    conditional(nofw, "--nofw") +
+    conditional(norc, "--norc") +
+    /* Spliced alignment */
+    optional("--pen-cansplice", penCansplice) +
+    optional("--pen-noncansplice", penNoncansplice) +
+    optional("--pen-canintronlen", penCanintronlen) +
+    optional("--pen-noncanintronlen", penNoncanintronlen) +
+    optional("--min-intronlen", minIntronlen) +
+    optional("--max-intronlen", maxIntronlen) +
+    optional("--known-splicesite-infile", knownSplicesiteInfile) +
+    optional("--novel-splicesite-outfile", novelSplicesiteOutfile) +
+    optional("--novel-splicesite-infile", novelSplicesiteInfile) +
+    conditional(noTempSplicesite, "--no-temp-splicesite") +
+    conditional(noSplicedAlignment, "--no-spliced-alignment") +
+    optional("--rna-strandness", rnaStrandness) +
+    conditional(tmo, "--tmo") +
+    conditional(dta, "--dta") +
+    conditional(dtaCufflinks, "--dta-cufflinks") +
+    /* Scoring */
+    optional("--ma", ma) +
+    optional("--mp", mp) +
+    optional("--np", np) +
+    optional("--sp", sp) +
+    optional("--rdg", rdg) +
+    optional("--rfg", rfg) +
+    optional("--score-min", scoreMin) +
+    /* Reporting */
+    optional("-k", k) +
+    optional("--all", all) +
+    /* Paired End */
+    conditional(fr, "--fr") +
+    conditional(rf, "--rf") +
+    conditional(ff, "--ff") +
+    conditional(noMixed, "--no-mixed") +
+    conditional(noDiscordant, "--no-discordant") +
+    /* Output */
+    conditional(time, "--time") +
+    optional("--un", un) +
+    optional("--al", al) +
+    optional("--un-conc", unConc) +
+    optional("--al-conc", alConc) +
+    optional("--un-gz", unGz) +
+    optional("--al-gz", alGz) +
+    optional("--un-conc-gz", unConcGz) +
+    optional("--al-conc-gz", alConcGz) +
+    optional("--un-bz2", unBz2) +
+    optional("--al-bz2", alBz2) +
+    optional("--un-conc-bz2", unConcBz2) +
+    optional("--al-conc-bz2", alConcBz2) +
+    conditional(quiet, "--quiet") +
+    optional("--met-file", metFile) +
+    conditional(metStderr, "--met-stderr") +
+    optional("--met", met) +
+    conditional(noHead, "--no-head") +
+    conditional(noSq, "--no-sq") +
+    optional("--rg-id", rgId) +
+    repeat("--rg", rg) +
+    conditional(omitSecSeq, "--omit-sec-seq") +
+    /* Performance */
+    optional("--offrate", offrate) +
+    optional("--threads", threads) +
+    conditional(reorder, "--reorder") +
+    conditional(mm, "--mm") +
+    /* Other */
+    conditional(qcFilter, "--qc-filter") +
+    optional("--seed", seed) +
+    conditional(nonDeterministic, "--non-deterministic") +
+    conditional(removeChrName, "--remove-chrname") +
+    conditional(addChrName, "--add-chrname") +
+    /* Required */
+    required("-x", hisat2Index) +
+    (R2 match {
+      case Some(r2)  => required("-1", R1) + optional("-2", r2)
+      case otherwise => required("-U", R1)
+    }) +
+    (if (outputAsStsout) "" else required("-S", output))
+}