dagr.tasks.jeanluc.GenerateRegionsFromFasta.scala Maven / Gradle / Ivy

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A set of example dagr tasks.

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/*
 * The MIT License
 *
 * Copyright (c) 2016 Fulcrum Genomics LLC
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package dagr.tasks.jeanluc

import dagr.core.execsystem.{Cores, Memory}
import dagr.tasks.DagrDef
import DagrDef.PathToFasta

import scala.collection.mutable.ListBuffer

/** Tool to generate FreeBayes/bamtools region lists from a FASTA, for use when parallelizing FreeBayes. */
class GenerateRegionsFromFasta(ref: PathToFasta,
                               regionSize: Option[Int] = None) extends JeanLucTask {
  requires(Cores(1), Memory("1G"))

  override def addJeanLucArgs(buffer: ListBuffer[Any]): Unit = {
    buffer.append("INPUT=" + ref)
    regionSize.foreach(rs => buffer.append("REGION_SIZE=" + rs))
  }
}