Add BWA runner.

src/main/scala/org/bdgenomics/cannoli/Bwa.scala

@@ -0,0 +1,114 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.cannoli
+
+import htsjdk.samtools.ValidationStringency
+import org.apache.spark.SparkContext
+import org.apache.spark.SparkContext._
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
+import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.utils.cli._
+import org.bdgenomics.utils.misc.Logging
+import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
+
+object Bwa extends BDGCommandCompanion {
+  val commandName = "bwa"
+  val commandDescription = "ADAM Pipe API wrapper for Bwa."
+
+  def apply(cmdLine: Array[String]) = {
+    new Bwa(Args4j[BwaArgs](cmdLine))
+  }
+}
+
+class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in interleaved FASTQ format", index = 0)
+  var inputPath: String = null
+
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to", index = 1)
+  var outputPath: String = null
+
+  @Argument(required = true, metaVar = "SAMPLE", usage = "Sample ID", index = 2)
+  var sample: String = null
+
+  @Args4jOption(required = true, name = "-index", usage = "Path to the bwa index to be searched, e.g. <ebwt> in bwa [options]* <ebwt> ...")
+  var indexPath: String = null
+
+  @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file")
+  var asSingleFile: Boolean = false
+
+  @Args4jOption(required = false, name = "-defer_merging", usage = "Defers merging single file output")
+  var deferMerging: Boolean = false
+
+  @Args4jOption(required = false, name = "-bwa_path", usage = "Path to the BWA executable.")
+  var bwaPath: String = _
+
+  @Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c..")
+  var dockerImage: String = "quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c"
+
+  @Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch BWA. If false, uses the BWA executable path.")
+  var useDocker: Boolean = _
+
+  // must be defined due to ADAMSaveAnyArgs, but unused here
+  var sortFastqOutput: Boolean = false
+}
+
+/**
+ * Bwa.
+ */
+class Bwa(protected val args: BwaArgs) extends BDGSparkCommand[BwaArgs] with Logging {
+  val companion = Bwa
+
+  def run(sc: SparkContext) {
+    val input: FragmentRDD = sc.loadFragments(args.inputPath)
+
+    implicit val tFormatter = InterleavedFASTQInFormatter
+    implicit val uFormatter = new AnySAMOutFormatter
+
+    val sample = args.sample
+
+    val bwaCommand = if (args.useDocker) {
+      Seq("docker",
+        "run",
+        args.dockerImage,
+        "mem",
+        "-t", "1",
+        "-R", s"@RG\\tID:${sample}\\tLB:${sample}\\tPL:ILLUMINA\\tPU:0\\tSM:${sample}",
+        "-p",
+        args.indexPath,
+        "-").mkString(" ")
+    } else {
+      require(args.bwaPath != null,
+        "-bwaPath must be defined if not using Docker.")
+      Seq(args.bwaPath,
+        "mem",
+        "-t", "1",
+        "-R", s"@RG\tID:${sample}\tLB:${sample}\tPL:ILLUMINA\tPU:0\tSM:${sample}",
+        "-p",
+        args.indexPath,
+        "-").mkString(" ")
+    }
+
+    val output: AlignmentRecordRDD = input.pipe[AlignmentRecord, AlignmentRecordRDD, InterleavedFASTQInFormatter](bwaCommand)
+
+    output.save(args)
+  }
+}

src/main/scala/org/bdgenomics/cannoli/Cannoli.scala

@@ -25,7 +25,7 @@ import org.bdgenomics.adam.cli.ADAMMain.defaultCommandGroups
  */
 object Cannoli {
   def main(args: Array[String]) {
-    val commandGroup = List(CommandGroup("CANNOLI", List(Bowtie, Bowtie2, Example, Freebayes, SnpEff)))
+    val commandGroup = List(CommandGroup("CANNOLI", List(Bowtie, Bowtie2, Bwa, Example, Freebayes, SnpEff)))
     new ADAMMain(defaultCommandGroups.union(commandGroup))(args)
   }
 }