[CANNOLI-110] Split commands with subcommands into separate Cannoli CLI classes.

README.md

@@ -36,12 +36,15 @@ Usage: cannoli-submit [<spark-args> --] <cannoli-args>
 Choose one of the following commands:
 
 CANNOLI
-            bedtools : ADAM Pipe API wrapper for Bedtools intersect.
+        bcftoolsNorm : ADAM Pipe API wrapper for BCFtools norm.
+   bedtoolsIntersect : ADAM Pipe API wrapper for Bedtools intersect.
               bowtie : ADAM Pipe API wrapper for Bowtie.
-             bowtie2 : ADAM Pipe API wrapper for Bowtie2.
+             bowtie2 : ADAM Pipe API wrapper for Bowtie 2.
                  bwa : ADAM Pipe API wrapper for BWA.
            freebayes : ADAM Pipe API wrapper for Freebayes.
+     samtoolsMpileup : ADAM Pipe API wrapper for samtools mpileup.
               snpEff : ADAM Pipe API wrapper for SnpEff.
+         vtNormalize : ADAM Pipe API wrapper for vt normalize.
 
 CANNOLI TOOLS
      interleaveFastq : Interleaves two FASTQ files.
@@ -65,7 +68,7 @@ $ ./bin/cannoli-submit \
     -add_indices
 ```
 
-or can be run using Docker.
+or can be run using Docker
 
 ```
 $ ./bin/cannoli-submit \
@@ -79,6 +82,24 @@ $ ./bin/cannoli-submit \
     -sequence_dictionary hg38.dict \
     -fragments \
     -use_docker \
-    -docker_image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
+    -image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
+    -add_indices
+```
+
+or can be run using Singularity
+
+```
+$ ./bin/cannoli-submit \
+    <spark-args>
+    -- \
+    bwa \
+    sample.unaligned.fragments.adam \
+    sample.bwa.hg38.alignments.adam \
+    sample \
+    -index hg38.fa \
+    -sequence_dictionary hg38.dict \
+    -fragments \
+    -use_singularity \
+    -image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
     -add_indices
 ```

cli/src/main/scala/org/bdgenomics/cannoli/cli/Bcftools.scala → cli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsNorm.scala

@@ -36,9 +36,9 @@ import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 import scala.collection.JavaConversions._
 
 /**
- * Bcftools function arguments.
+ * Bcftools norm function arguments.
  */
-class BcftoolsFnArgs extends Args4jBase {
+class BcftoolsNormFnArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the BCFtools executable. Defaults to bcftools.")
   var executable: String = "bcftools"
 
@@ -62,14 +62,14 @@ class BcftoolsFnArgs extends Args4jBase {
 }
 
 /**
- * Bcftools wrapper as a function VariantContextRDD → VariantContextRDD,
+ * Bcftools norm wrapper as a function VariantContextRDD → VariantContextRDD,
  * for use in cannoli-shell or notebooks.
  *
- * @param args Bcftools function arguments.
+ * @param args Bcftools norm function arguments.
  * @param sc Spark context.
  */
-class BcftoolsFn(
-    val args: BcftoolsFnArgs,
+class BcftoolsNormFn(
+    val args: BcftoolsNormFnArgs,
     sc: SparkContext) extends CannoliFn[VariantContextRDD, VariantContextRDD](sc) with Logging {
 
   override def apply(variantContexts: VariantContextRDD): VariantContextRDD = {
@@ -105,19 +105,19 @@ class BcftoolsFn(
   }
 }
 
-object Bcftools extends BDGCommandCompanion {
-  val commandName = "bcftools"
+object BcftoolsNorm extends BDGCommandCompanion {
+  val commandName = "bcftoolsNorm"
   val commandDescription = "ADAM Pipe API wrapper for BCFtools norm."
 
   def apply(cmdLine: Array[String]) = {
-    new Bcftools(Args4j[BcftoolsArgs](cmdLine))
+    new BcftoolsNorm(Args4j[BcftoolsNormArgs](cmdLine))
   }
 }
 
 /**
- * Bcftools command line arguments.
+ * Bcftools norm command line arguments.
  */
-class BcftoolsArgs extends BcftoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs {
+class BcftoolsNormArgs extends BcftoolsNormFnArgs with ADAMSaveAnyArgs with ParquetArgs {
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
   var inputPath: String = null
 
@@ -141,15 +141,15 @@ class BcftoolsArgs extends BcftoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs
 }
 
 /**
- * Bcftools command line wrapper.
+ * Bcftools norm command line wrapper.
  */
-class Bcftools(protected val args: BcftoolsArgs) extends BDGSparkCommand[BcftoolsArgs] with Logging {
-  val companion = Bcftools
+class BcftoolsNorm(protected val args: BcftoolsNormArgs) extends BDGSparkCommand[BcftoolsNormArgs] with Logging {
+  val companion = BcftoolsNorm
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
     val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
-    val pipedVariantContexts = new BcftoolsFn(args, sc).apply(variantContexts)
+    val pipedVariantContexts = new BcftoolsNormFn(args, sc).apply(variantContexts)
     pipedVariantContexts.saveAsVcf(args, stringency)
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala → cli/src/main/scala/org/bdgenomics/cannoli/cli/BedtoolsIntersect.scala

@@ -36,9 +36,9 @@ import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 import scala.collection.JavaConversions._
 
 /**
- * Bedtools function arguments.
+ * Bedtools intersect function arguments.
  */
-class BedtoolsFnArgs extends Args4jBase {
+class BedtoolsIntersectFnArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-a", usage = "Bedtools intersect -a option. One of {-a,-b} should be left unspecified to accept piped input.")
   var a: String = null
 
@@ -68,22 +68,22 @@ class BedtoolsFnArgs extends Args4jBase {
 }
 
 /**
- * Bedtools wrapper as a function FeatureRDD → FeatureRDD,
+ * Bedtools intersect wrapper as a function FeatureRDD → FeatureRDD,
  * for use in cannoli-shell or notebooks.
  *
  * <code>
- * val args = new BedtoolsFnArgs()
+ * val args = new BedtoolsIntersectFnArgs()
  * args.b = "foo.bed"
  * args.useDocker = true
  * val features = ...
- * val pipedFeatures = new BedtoolsFn(args, sc).apply(features)
+ * val pipedFeatures = new BedtoolsIntersectFn(args, sc).apply(features)
  * </code>
  *
- * @param args Bedtools function arguments.
+ * @param args Bedtools intersect function arguments.
  * @param sc Spark context.
  */
-class BedtoolsFn(
-    val args: BedtoolsFnArgs,
+class BedtoolsIntersectFn(
+    val args: BedtoolsIntersectFnArgs,
     sc: SparkContext) extends CannoliFn[FeatureRDD, FeatureRDD](sc) with Logging {
 
   override def apply(features: FeatureRDD): FeatureRDD = {
@@ -125,19 +125,19 @@ class BedtoolsFn(
   }
 }
 
-object Bedtools extends BDGCommandCompanion {
-  val commandName = "bedtools"
+object BedtoolsIntersect extends BDGCommandCompanion {
+  val commandName = "bedtoolsIntersect"
   val commandDescription = "ADAM Pipe API wrapper for Bedtools intersect."
 
   def apply(cmdLine: Array[String]) = {
-    new Bedtools(Args4j[BedtoolsArgs](cmdLine))
+    new BedtoolsIntersect(Args4j[BedtoolsIntersectArgs](cmdLine))
   }
 }
 
 /**
- * Bedtools command line arguments.
+ * Bedtools intersect command line arguments.
  */
-class BedtoolsArgs extends BedtoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs {
+class BedtoolsIntersectArgs extends BedtoolsIntersectFnArgs with ADAMSaveAnyArgs with ParquetArgs {
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe features from (e.g., .bed, .gff/.gtf, .gff3, .interval_list, .narrowPeak). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
@@ -164,10 +164,10 @@ class BedtoolsArgs extends BedtoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs
 }
 
 /**
- * Bedtools command line wrapper.
+ * Bedtools intersect command line wrapper.
  */
-class Bedtools(protected val args: BedtoolsArgs) extends BDGSparkCommand[BedtoolsArgs] with Logging {
-  val companion = Bedtools
+class BedtoolsIntersect(protected val args: BedtoolsIntersectArgs) extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging {
+  val companion = BedtoolsIntersect
 
   override def run(sc: SparkContext) {
     val projection = Projection(
@@ -184,7 +184,7 @@ class Bedtools(protected val args: BedtoolsArgs) extends BDGSparkCommand[Bedtool
       optMinPartitions = Option(args.partitions),
       optProjection = if (args.limitProjection) Some(projection) else None
     )
-    val pipedFeatures = new BedtoolsFn(args, sc).apply(features)
+    val pipedFeatures = new BedtoolsIntersectFn(args, sc).apply(features)
 
     pipedFeatures.save(args.outputPath,
       asSingleFile = args.asSingleFile,

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

@@ -28,15 +28,15 @@ import org.bdgenomics.utils.cli._
 
 object Cannoli {
 
-  val defaultCommandGroups = List(CommandGroup("CANNOLI", List(Bcftools,
-    Bedtools,
+  val defaultCommandGroups = List(CommandGroup("CANNOLI", List(BcftoolsNorm,
+    BedtoolsIntersect,
     Bowtie,
     Bowtie2,
     Bwa,
     Freebayes,
-    Samtools,
+    SamtoolsMpileup,
     SnpEff,
-    Vt)),
+    VtNormalize)),
     CommandGroup("CANNOLI TOOLS", List(InterleaveFastq,
       SampleReads)))
 

cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala → cli/src/main/scala/org/bdgenomics/cannoli/cli/SamtoolsMpileup.scala

@@ -34,9 +34,9 @@ import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 import scala.collection.JavaConversions._
 
 /**
- * Samtools function arguments.
+ * Samtools mpileup function arguments.
  */
-class SamtoolsFnArgs extends Args4jBase {
+class SamtoolsMpileupFnArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the samtools executable. Defaults to samtools.")
   var executable: String = "samtools"
 
@@ -60,14 +60,14 @@ class SamtoolsFnArgs extends Args4jBase {
 }
 
 /**
- * Samtools wrapper as a function AlignmentRecordRDD → VariantContextRDD,
+ * Samtools mpileup wrapper as a function AlignmentRecordRDD → VariantContextRDD,
  * for use in cannoli-shell or notebooks.
  *
- * @param args Samtools function arguments.
+ * @param args Samtools mpileup function arguments.
  * @param sc Spark context.
  */
-class SamtoolsFn(
-    val args: SamtoolsFnArgs,
+class SamtoolsMpileupFn(
+    val args: SamtoolsMpileupFnArgs,
     sc: SparkContext) extends CannoliFn[AlignmentRecordRDD, VariantContextRDD](sc) with Logging {
 
   override def apply(alignments: AlignmentRecordRDD): VariantContextRDD = {
@@ -106,19 +106,19 @@ class SamtoolsFn(
   }
 }
 
-object Samtools extends BDGCommandCompanion {
-  val commandName = "samtools"
+object SamtoolsMpileup extends BDGCommandCompanion {
+  val commandName = "samtoolsMpileup"
   val commandDescription = "ADAM Pipe API wrapper for samtools mpileup."
 
   def apply(cmdLine: Array[String]) = {
-    new Samtools(Args4j[SamtoolsArgs](cmdLine))
+    new SamtoolsMpileup(Args4j[SamtoolsMpileupArgs](cmdLine))
   }
 }
 
 /**
- * Samtools command line arguments.
+ * Samtools mpileup command line arguments.
  */
-class SamtoolsArgs extends SamtoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs {
+class SamtoolsMpileupArgs extends SamtoolsMpileupFnArgs with ADAMSaveAnyArgs with ParquetArgs {
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe alignment records from (e.g. .bam, .cram, .sam). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
@@ -142,15 +142,15 @@ class SamtoolsArgs extends SamtoolsFnArgs with ADAMSaveAnyArgs with ParquetArgs
 }
 
 /**
- * Samtools command line wrapper.
+ * Samtools mpileup command line wrapper.
  */
-class Samtools(protected val args: SamtoolsArgs) extends BDGSparkCommand[SamtoolsArgs] with Logging {
-  val companion = Samtools
+class SamtoolsMpileup(protected val args: SamtoolsMpileupArgs) extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging {
+  val companion = SamtoolsMpileup
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
     val alignments = sc.loadAlignments(args.inputPath, stringency = stringency)
-    val variantContexts = new SamtoolsFn(args, sc).apply(alignments)
+    val variantContexts = new SamtoolsMpileupFn(args, sc).apply(alignments)
 
     if (isVcfExt(args.outputPath)) {
       variantContexts.saveAsVcf(

cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala → cli/src/main/scala/org/bdgenomics/cannoli/cli/VtNormalize.scala

@@ -36,9 +36,9 @@ import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 import scala.collection.JavaConversions._
 
 /**
- * Vt function arguments.
+ * Vt normalize function arguments.
  */
-class VtFnArgs extends Args4jBase {
+class VtNormalizeFnArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the vt executable. Defaults to vt.")
   var executable: String = "vt"
 
@@ -65,14 +65,14 @@ class VtFnArgs extends Args4jBase {
 }
 
 /**
- * Vt wrapper as a function VariantContextRDD → VariantContextRDD,
+ * Vt normalize wrapper as a function VariantContextRDD → VariantContextRDD,
  * for use in cannoli-shell or notebooks.
  *
- * @param args Vt function arguments.
+ * @param args Vt normalize function arguments.
  * @param sc Spark context.
  */
-class VtFn(
-    val args: VtFnArgs,
+class VtNormalizeFn(
+    val args: VtNormalizeFnArgs,
     sc: SparkContext) extends CannoliFn[VariantContextRDD, VariantContextRDD](sc) with Logging {
 
   override def apply(variantContexts: VariantContextRDD): VariantContextRDD = {
@@ -108,19 +108,19 @@ class VtFn(
   }
 }
 
-object Vt extends BDGCommandCompanion {
-  val commandName = "vt"
+object VtNormalize extends BDGCommandCompanion {
+  val commandName = "vtNormalize"
   val commandDescription = "ADAM Pipe API wrapper for vt normalize."
 
   def apply(cmdLine: Array[String]) = {
-    new Vt(Args4j[VtArgs](cmdLine))
+    new VtNormalize(Args4j[VtNormalizeArgs](cmdLine))
   }
 }
 
 /**
- * Vt command line arguments.
+ * Vt normalize command line arguments.
  */
-class VtArgs extends VtFnArgs with ADAMSaveAnyArgs with ParquetArgs {
+class VtNormalizeArgs extends VtNormalizeFnArgs with ADAMSaveAnyArgs with ParquetArgs {
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
   var inputPath: String = null
 
@@ -144,15 +144,15 @@ class VtArgs extends VtFnArgs with ADAMSaveAnyArgs with ParquetArgs {
 }
 
 /**
- * Vt command line wrapper.
+ * Vt normalize command line wrapper.
  */
-class Vt(protected val args: VtArgs) extends BDGSparkCommand[VtArgs] with Logging {
-  val companion = Vt
+class VtNormalize(protected val args: VtNormalizeArgs) extends BDGSparkCommand[VtNormalizeArgs] with Logging {
+  val companion = VtNormalize
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
     val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
-    val pipedVariantContexts = new VtFn(args, sc).apply(variantContexts)
+    val pipedVariantContexts = new VtNormalizeFn(args, sc).apply(variantContexts)
     pipedVariantContexts.saveAsVcf(args, stringency)
   }
 }