diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index 22063d335312ce16ea3acfbc37775ada3b0032ef..035194d4836da5f9da66dc3e7328bfc7a1303131 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -25,7 +25,7 @@ import scala.io.Source
/**
* General picard extension
*
- * This is based on using class files directly from the jar
+ * This is based on using class files directly from the jar, if needed other picard jar can be used
*/
abstract class Picard extends BiopetJavaCommandLineFunction {
override def subPath = "picard" :: super.subPath
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
index a6fe688c2486f46701d6397c8fcffacee4b1c29c..a2804668e5b77e71d8d2793aaaf80bdd7e68c646 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction {
override val defaultVmem = "4G"
override val defaultThreads = 2
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
index 5be51decae455e3ff1a06c2379ee12b836a1c745..f324001077ac6c9d8b544783aa01c7f8f2dad190 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for sambemba flagstat */
class SambambaFlagstat(val root: Configurable) extends Sambamba {
override val defaultThreads = 2
@@ -28,6 +29,7 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
@Output(doc = "output File")
var output: File = _
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("flagstat") +
optional("-t", nCoresRequest) +
@@ -35,24 +37,3 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
" > " +
required(output)
}
-
-object SambambaFlagstat {
- def apply(root: Configurable, input: File, output: File): SambambaFlagstat = {
- val flagstat = new SambambaFlagstat(root)
- flagstat.input = input
- flagstat.output = output
- return flagstat
- }
-
- def apply(root: Configurable, input: File, outputDir: String): SambambaFlagstat = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): SambambaFlagstat = {
- return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".flagstat"
-}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
index 4d988ef13c93074ff2ecc842be6aed69be07676a..924a420b44eb878d8a53d888eabe6a1daa2a61d5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for sambemba index */
class SambambaIndex(val root: Configurable) extends Sambamba {
override val defaultThreads = 2
@@ -28,30 +29,10 @@ class SambambaIndex(val root: Configurable) extends Sambamba {
@Output(doc = "Output .bai file to")
var output: File = _
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("index") +
optional("-t", nCoresRequest) +
required(input) +
required(output)
}
-
-object SambambaIndex {
- def apply(root: Configurable, input: File, output: File): SambambaIndex = {
- val flagstat = new SambambaIndex(root)
- flagstat.input = input
- flagstat.output = output
- return flagstat
- }
-
- def apply(root: Configurable, input: File, outputDir: String): SambambaIndex = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): SambambaIndex = {
- return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
-}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
index a45bc73f43fa56a1968487e18e09e0c4d38f129d..bb4ec3ef2f064abad45108be8a33e47fffb9963e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for sambemba markdup */
class SambambaMarkdup(val root: Configurable) extends Sambamba {
override val defaultThreads = 4
@@ -36,6 +37,7 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
val overflow_list_size: Option[Int] = config("overflow-list-size", default = 200000)
val io_buffer_size: Option[Int] = config("io-buffer-size", default = 128)
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("markdup") +
conditional(remove_duplicates, "--remove-duplicates") +
@@ -47,24 +49,3 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
required(input) +
required(output)
}
-
-object SambambaMarkdup {
- def apply(root: Configurable, input: File, output: File): SambambaMarkdup = {
- val flagstat = new SambambaMarkdup(root)
- flagstat.input = input
- flagstat.output = output
- return flagstat
- }
-
- def apply(root: Configurable, input: File, outputDir: String): SambambaMarkdup = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): SambambaMarkdup = {
- return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
-}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
index 45af3a8c387fdf5bcac8f10e2b5c9a98c912f062..8b514317a1980106c2d9b63e09d98e929c84904e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for sambemba merge */
class SambambaMerge(val root: Configurable) extends Sambamba {
override val defaultThreads = 4
@@ -31,6 +32,7 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val compression_level: Option[Int] = config("compression_level", default = 6)
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("merge") +
optional("-t", nCoresRequest) +
@@ -38,36 +40,3 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
required(output) +
repeat("", input)
}
-
-object SambambaMerge {
- def apply(root: Configurable, input: List[File], output: File): SambambaMerge = {
- val flagstat = new SambambaMerge(root)
- flagstat.input = input
- flagstat.output = output
- return flagstat
- }
-
- def apply(root: Configurable, input: List[File], outputDir: String): SambambaMerge = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.head.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: List[File]): SambambaMerge = {
- return apply(root, input, new File(swapExtension(input.head.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".merge.bam"
-}
-
-//
-//object MergeSamFiles {
-// def apply(root: Configurable, input: List[File], outputDir: String, sortOrder: String = null): MergeSamFiles = {
-// val mergeSamFiles = new MergeSamFiles(root)
-// mergeSamFiles.input = input
-// mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
-// if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
-// else mergeSamFiles.sortOrder = sortOrder
-// return mergeSamFiles
-// }
-//}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
index 740da10524d33f6e5e370bdc3320defa50f7ee79..d220be089572d7988f6c12c315620d35b211beea 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+/** General class for samtools extensions */
abstract class Samtools extends BiopetCommandLineFunction {
override def subPath = "samtools" :: super.subPath
executable = config("exe", default = "samtools")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
index a4833d5f17c509fc0a47ca77a631e2ec32596bd1..67fd2f333d55ae5a30715bbb15a3132999c16aac 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for samtools flagstat */
class SamtoolsFlagstat(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
@@ -26,6 +27,7 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
@Output(doc = "output File")
var output: File = _
+ /** Returns command to execute */
def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
index b8a3a2d0e6ec913611abe21b00c1dfe200842418..9cc5d655f0d3b5a50178bef5e284c6d61503372a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for samtools mpileup */
class SamtoolsMpileup(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
@@ -45,6 +46,8 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
conditional(disableBaq, "-B")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + required(input)
+
+ /** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
index 883c21ac1ff2bb0940d2e61fdb13486829454dee..5dcc66ee16e4f885227db0d97d435ec972300fe2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for samtools view */
class SamtoolsView(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
@@ -37,6 +38,8 @@ class SamtoolsView(val root: Configurable) extends Samtools {
conditional(h, "-h")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + required(input)
+
+ /** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
index a1131371ade82303aca47155593568f2cadbeb2d..c12ca6c5f5f8c822fe0206c189485a2e7957bfc6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
@@ -17,9 +17,7 @@ package nl.lumc.sasc.biopet.extensions.seqtk
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-/**
- * Abstract class for all seqtk wrappers.
- */
+/** Abstract class for all seqtk wrappers. */
abstract class Seqtk extends BiopetCommandLineFunction {
override def subPath = "seqtk" :: super.subPath
executable = config("exe", default = "seqtk", freeVar = true)