dagr.tasks.picard.CheckIlluminaDirectory.scala Maven / Gradle / Ivy

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A set of example dagr tasks.

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/*
 * The MIT License
 *
 * Copyright (c) 2017 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.picard

import dagr.tasks.DagrDef.DirPath
import scala.collection.mutable.ListBuffer

class CheckIlluminaDirectory(basecallsDir: DirPath,
                             lanes: Seq[Int],
                             readStructure: String,
                             linkLocs: Boolean = false
                            ) extends PicardTask {

  override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = {
    buffer += "BASECALLS_DIR=" + basecallsDir
    buffer += "READ_STRUCTURE=" + readStructure
    buffer += "LINK_LOCS=" + linkLocs
    lanes.foreach(buffer += "LANES=" + _)
  }
}