diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
new file mode 100644
index 0000000000000000000000000000000000000000..9185e739305517b0954917de0d53e6942131bfdd
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
@@ -0,0 +1,66 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2015 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+/**
+ * Wrapper for the Cnmops command line tool.
+ * Written based on Cnmops version v2.2.1.
+ */
+class Cnmops(val root: Configurable) extends BiopetJavaCommandLineFunction {
+ javaMainClass = getClass.getName
+
+ /** input file */
+ @Input(doc = "Input file BAM", required = true)
+ var input: List[File] = List()
+
+ /** output files, computed automatically from output directory */
+
+ @Output(doc = "Output CNV file")
+ lazy val output_cnv: File = {
+ if (output_dir == null)
+ throw new RuntimeException("Unexpected error when trying to set cn.MOPS CNV output")
+ new File(output_dir, "cnv.txt")
+ }
+ @Output(doc = "Output CNR file")
+ lazy val output_cnr: File = {
+ if (output_dir == null)
+ throw new RuntimeException("Unexpected error when trying to set cn.MOPS CNR output")
+ new File(output_dir, "cnr.txt")
+ }
+
+ /** write all output files to this directory [./] */
+ var output_dir: String = _
+
+ override def beforeGraph = {
+ super.beforeGraph
+ require(!output_dir.isEmpty, "Outputdir for cn.MOPS should not be empty")
+ require(input.length > 1, "Please supply at least 2 BAM files for cn.MOPS")
+ }
+
+ override val versionRegex = """Cnmops v(.*)""".r
+ override def versionCommand = executable
+
+ def cmdLine = {
+ required(executable) +
+ required("--output-dir", output_dir) +
+ required(input)
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f55a7f2ef74be813233553a6f1debb2c76fb3b79
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
@@ -0,0 +1,34 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+ * Created by wyleung on 17-2-15.
+ */
+trait RscriptCommandLineFunction extends BiopetCommandLineFunction{
+ @Input(doc = "R script", required = false)
+ var script: File = _
+ protected var scriptName: String = _
+
+ executable = config("exe", default = "Rscript", submodule = "R")
+
+
+ /**
+ * Set the Rscript to run
+ *
+ * @param filename RScript file location
+ */
+ def setScript(filename: File) = {
+
+
+ }
+
+ def setScript(filename: File, subpackage: String) = {
+
+
+ }
+
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
index 5227fc289a0ac72a9782759e4e67f88bb3474ab6..d55ddeed838a896749023a7bc168b211a961fdcc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConverters._
import scala.collection.mutable
-import scala.collection.immutable.{ Map }
+import scala.collection.immutable.Map
import scala.io.Source
import scala.language.postfixOps
@@ -32,20 +32,20 @@ class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Input FASTQ", shortName = "input", required = true)
- var input: File = _
+ var input: File = null
@Output(doc = "Output JSON", shortName = "output", required = true)
- var output: File = _
+ var output: File = null
override val defaultVmem = "4G"
memoryLimit = Option(3.0)
override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
- def getSummary: Json = {
+ def summary: Json = {
val json = Parse.parseOption(Source.fromFile(output).mkString)
- if (json.isEmpty) return jNull
- else return json.get.fieldOrEmptyObject("stats")
+ if (json.isEmpty) jNull
+ else json.get.fieldOrEmptyObject("stats")
}
}
@@ -61,7 +61,7 @@ object Seqstat extends ToolCommand {
val seqstat = new Seqstat(root)
seqstat.input = input
seqstat.output = output
- return seqstat
+ seqstat
}
def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
@@ -69,7 +69,7 @@ object Seqstat extends ToolCommand {
val ext = fastqfile.getName.substring(fastqfile.getName.lastIndexOf("."))
seqstat.input = fastqfile
seqstat.output = new File(outDir + fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
- return seqstat
+ seqstat
}
def mergeSummaries(jsons: List[Json]): Json = {
@@ -101,7 +101,7 @@ object Seqstat extends ToolCommand {
val reads = json.fieldOrEmptyObject("reads")
addJson(reads, readsTotal)
}
- return ("bases" := (
+ ("bases" := (
("num_n" := basesTotal("num_n")) ->:
("num_total" := basesTotal("num_total")) ->:
("num_qual_gte" := (
@@ -254,7 +254,7 @@ object Seqstat extends ToolCommand {
}
// implicit conversion to Int using foldLeft(0)
- val avgQual: Int = (readQual.foldLeft(0)(_ + _) / readQual.length)
+ val avgQual: Int = (readQual.sum / readQual.length)
if (readStats.qual.length <= avgQual) {
readStats.qual ++= mutable.ArrayBuffer.fill(avgQual - readStats.qual.length + 1)(0)
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index fbdb8fc166443b1cd580f9864f490deeb51fa1b0..4551db8fb92be9bda573f30f171367ab10dd5366 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -149,25 +149,25 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
}
def seqstatSummary(): Option[Json] = {
- val R1_chunks = for ((key, value) <- chunks) yield value.seqstatR1.getSummary
+ val R1_chunks = for ((key, value) <- chunks) yield value.seqstatR1.summary
val R1: Json = Seqstat.mergeSummaries(R1_chunks.toList)
val R2: Option[Json] = if (!flexiprep.paired) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.getSummary)
+ else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.summary)
else {
- val s = for ((key, value) <- chunks) yield value.seqstatR2.getSummary
+ val s = for ((key, value) <- chunks) yield value.seqstatR2.summary
Option(Seqstat.mergeSummaries(s.toList))
}
val R1_proc: Option[Json] = if (flexiprep.skipClip && flexiprep.skipTrim) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR1after.getSummary)
+ else if (chunks.size == 1) Option(chunks.head._2.seqstatR1after.summary)
else {
- val s = for ((key, value) <- chunks) yield value.seqstatR1after.getSummary
+ val s = for ((key, value) <- chunks) yield value.seqstatR1after.summary
Option(Seqstat.mergeSummaries(s.toList))
}
val R2_proc: Option[Json] = if (!flexiprep.paired || (flexiprep.skipClip && flexiprep.skipTrim)) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR2after.getSummary)
+ else if (chunks.size == 1) Option(chunks.head._2.seqstatR2after.summary)
else {
- val s = for ((key, value) <- chunks) yield value.seqstatR2after.getSummary
+ val s = for ((key, value) <- chunks) yield value.seqstatR2after.summary
Option(Seqstat.mergeSummaries(s.toList))
}
return Option(("R1_raw" := R1) ->: