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A set of example dagr tasks.
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/*
 * The MIT License
 *
 * Copyright (c) $year Fulcrum Genomics
 *
 * 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

import dagr.core.tasksystem.{Dependable, EmptyDependable}

/**
  * Object that is designed to be imported with `import DagrDef._` in any/all classes
  * much like the way that scala.PreDef is imported in all files automatically.
  *
  * New methods, types and objects should not be added to this class lightly as they
  * will pollute the namespace of any classes which import it.
  */
object DagrDef {

  /////////////////////////////////////////////////////////////////////////////
  // Path-like typedefs that are used to hint at what the Path should be to
  /////////////////////////////////////////////////////////////////////////////

  /** Represents a path to a BAM (or SAM or CRAM) index file. */
  type PathToBai = java.nio.file.Path

  /** Represents a path to a BAM (or SAM or CRAM) file. */
  type PathToBam = java.nio.file.Path

  /** Represents a path to an intervals file (IntervalList or BED). */
  type PathToIntervals = java.nio.file.Path

  /** Represents a path to a FASTQ file (optionally gzipped). */
  type PathToFastq = java.nio.file.Path

  /** Represents a path to a Reference FASTA file. */
  type PathToFasta = java.nio.file.Path

  /** Represents a path to a VCF/BCF/VCF.gz. */
  type PathToVcf = java.nio.file.Path

  /** Represents a full path including directories, that is intended to be used as a prefix for generating file paths. */
  type PathPrefix = java.nio.file.Path

  /** Represents a path to directory. */
  type DirPath = java.nio.file.Path

  /** Represents a path to a file (not a directory) that doesn't have a more specific type. */
  type FilePath = java.nio.file.Path

  /** A String that represents the prefix or basename of a filename. */
  type FilenamePrefix = String

  /** Implicit that will convert an Option[Dependable] to a Dependable when needed. */
  implicit def optionDependableToDependable(maybe: Option[Dependable]): Dependable = EmptyDependable.optionDependableToDependable(maybe)
}