diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 911a8349d502ad6bc63588a19acad7575d2fe181..503f67e308f1b9e7a9e613ce298159215a227621 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -77,7 +77,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
List(bamFile)
} else {
- val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+ val markDup = MarkDuplicates(this, files, new File(outputDir, outputName + ".dedup.bam"))
markDup.isIntermediate = useIndelRealigner
add(markDup)
if (useIndelRealigner) {
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index 79dfe02f8ad64c2c0cc0923e78d6df9651272438..60f9b10ff1aed9748e40716d16e5fd73537d5fa4 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
@@ -129,7 +129,7 @@ trait BastyTrait extends MultiSampleQScript {
raxmlBoot.N = Some(1)
raxmlBoot.n = outputName + "_boot_" + t
add(raxmlBoot)
- raxmlBoot.getBootstrapFile
+ raxmlBoot.getBootstrapFile.get
}
val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
@@ -138,7 +138,7 @@ trait BastyTrait extends MultiSampleQScript {
val raxmlBi = new Raxml(this)
raxmlBi.input = concensusVariants
raxmlBi.t = raxmlMl.getBestTreeFile
- raxmlBi.z = cat.output
+ raxmlBi.z = Some(cat.output)
raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBi.p = Some(seed)
raxmlBi.f = "b"
@@ -148,7 +148,7 @@ trait BastyTrait extends MultiSampleQScript {
val gubbins = new RunGubbins(this)
gubbins.fastafile = concensusVariants
- gubbins.startingTree = Some(raxmlBi.getBipartitionsFile)
+ gubbins.startingTree = raxmlBi.getBipartitionsFile
gubbins.outputDirectory = dirSufixGubbins
add(gubbins)
}
diff --git a/public/biopet-framework/nb-configuration.xml b/public/biopet-framework/nb-configuration.xml
deleted file mode 100644
index bf0170b5b027d741082d582f5e56636c6e5e3605..0000000000000000000000000000000000000000
--- a/public/biopet-framework/nb-configuration.xml
+++ /dev/null
@@ -1,46 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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 2014 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.
-
--->
-<project-shared-configuration>
- <!--
-This file contains additional configuration written by modules in the NetBeans IDE.
-The configuration is intended to be shared among all the users of project and
-therefore it is assumed to be part of version control checkout.
-Without this configuration present, some functionality in the IDE may be limited or fail altogether.
--->
- <config-data xmlns="http://www.netbeans.org/ns/maven-config-data/1">
- <configurations>
- <configuration id="yamsvp" profiles=""/>
- </configurations>
- </config-data>
- <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
- <!--
-Properties that influence various parts of the IDE, especially code formatting and the like.
-You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
-That way multiple projects can share the same settings (useful for formatting rules for example).
-Any value defined here will override the pom.xml file value but is only applicable to the current project.
--->
- <netbeans.hint.license>apache20</netbeans.hint.license>
- <com-junichi11-netbeans-changelf.enable>true</com-junichi11-netbeans-changelf.enable>
- <com-junichi11-netbeans-changelf.use-project>true</com-junichi11-netbeans-changelf.use-project>
- <com-junichi11-netbeans-changelf.lf-kind>LF</com-junichi11-netbeans-changelf.lf-kind>
- <com-junichi11-netbeans-changelf.use-global>false</com-junichi11-netbeans-changelf.use-global>
- <com-junichi11-netbeans-changelf.show-dialog>true</com-junichi11-netbeans-changelf.show-dialog>
- <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
- </properties>
-</project-shared-configuration>
diff --git a/public/biopet-framework/nbactions-yamsvp.xml b/public/biopet-framework/nbactions-yamsvp.xml
deleted file mode 100644
index 3eb4ab5ce9a85570326db29fef02b40dadd793b1..0000000000000000000000000000000000000000
--- a/public/biopet-framework/nbactions-yamsvp.xml
+++ /dev/null
@@ -1,67 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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 2014 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.
-
--->
-<actions>
- <action>
- <actionName>run</actionName>
- <preAction>build-with-dependencies</preAction>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
- <exec.executable>java</exec.executable>
- <exec.workingdir>../test</exec.workingdir>
- </properties>
- </action>
- <action>
- <actionName>debug</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
- <exec.executable>java</exec.executable>
- <jpda.listen>true</jpda.listen>
- <exec.workingdir>../test</exec.workingdir>
- </properties>
- </action>
- <action>
- <actionName>profile</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
- <exec.executable>java</exec.executable>
- <exec.workingdir>../test</exec.workingdir>
- </properties>
- </action>
- </actions>
diff --git a/public/biopet-framework/nbactions.xml b/public/biopet-framework/nbactions.xml
deleted file mode 100644
index cc2b2ad541a38f78e0eeae19913f68b8ce0f490b..0000000000000000000000000000000000000000
--- a/public/biopet-framework/nbactions.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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 2014 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.
-
--->
-<actions>
- <action>
- <actionName>run</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
- <exec.executable>java</exec.executable>
- <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
- </properties>
- </action>
- <action>
- <actionName>debug</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
- <exec.executable>java</exec.executable>
- <jpda.listen>true</jpda.listen>
- <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
- </properties>
- </action>
- <action>
- <actionName>profile</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
- </goals>
- <properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
- <exec.executable>java</exec.executable>
- <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
- </properties>
- </action>
- </actions>
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 115bca1b89aa8e6e7c41b48bce511e379de72a45..ba38670536bfc6e920513adf3aabb4ab247547f5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -25,9 +25,7 @@ import scala.util.matching.Regex
import java.io.FileInputStream
import java.security.MessageDigest
-/**
- * Biopet command line trait to auto check executable and cluster values
- */
+/** Biopet command line trait to auto check executable and cluster values */
trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
analysisName = configName
@@ -47,14 +45,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
*/
protected[core] def beforeCmd {}
- /**
- * Can override this method. This is executed after the script is done en queue starts to generate the graph
- */
+ /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
protected[core] def beforeGraph {}
- /**
- * Set default output file, threads and vmem for current job
- */
+ /** Set default output file, threads and vmem for current job */
override def freezeFieldValues() {
preProcesExecutable
beforeGraph
@@ -118,9 +112,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
}
- /**
- * executes checkExecutable method and fill job report
- */
+ /** executes checkExecutable method and fill job report */
final protected def preCmdInternal {
preProcesExecutable
@@ -133,10 +125,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
addJobReportBinding("version", getVersion)
}
- /**
- * Command to get version of executable
- * @return
- */
+ /** Command to get version of executable */
protected def versionCommand: String = null
/** Regex to get version from version command output */
@@ -146,10 +135,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected val versionExitcode = List(0)
/** Executes the version command */
- private def getVersionInternal: String = {
- if (versionCommand == null || versionRegex == null) return "N/A"
+ private def getVersionInternal: Option[String] = {
+ if (versionCommand == null || versionRegex == null) return None
val exe = new File(versionCommand.trim.split(" ")(0))
- if (!exe.exists()) return "N/A"
+ if (!exe.exists()) return None
val stdout = new StringBuffer()
val stderr = new StringBuffer()
def outputLog = "Version command: \n" + versionCommand +
@@ -158,25 +147,28 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
if (!versionExitcode.contains(process.exitValue)) {
logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
- return "N/A"
+ return None
}
for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
line match {
- case versionRegex(m) => return m
+ case versionRegex(m) => return Some(m)
case _ =>
}
}
logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
- return "N/A"
+ return None
}
/** Get version from cache otherwise execute the version command */
- def getVersion: String = {
+ def getVersion: Option[String] = {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
preProcesExecutable
- if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
- BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
- return BiopetCommandLineFunctionTrait.versionCache(executable)
+ if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
+ getVersionInternal match {
+ case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
+ case _ =>
+ }
+ BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
}
/**
@@ -205,9 +197,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
}
-/**
- * stores global caches
- */
+/** stores global caches */
object BiopetCommandLineFunctionTrait {
import scala.collection.mutable.Map
private val versionCache: Map[String, String] = Map()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index eb84ecbca9ed817c85a6e5c6920c4d887bf934d6..2e8c4002fb7e95404f41522ef970c84de9b50f63 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -57,12 +57,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
(for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
f match {
case f: BiopetJavaCommandLineFunction => {
- f.configName -> Map("version" -> f.getVersion,
+ f.configName -> Map("version" -> f.getVersion.getOrElse(None),
"java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
"jar_md5" -> SummaryQScript.md5sumCache.getOrElse(f.jarFile, None))
}
case f: BiopetCommandLineFunction => {
- f.configName -> Map("version" -> f.getVersion,
+ f.configName -> Map("version" -> f.getVersion.getOrElse(None),
"md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
}
case _ => throw new IllegalStateException("This should not be possible")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index ac1d2a7a8d6e1fc0666d20b6ddbbd361f05cd27d..ef8fb9d6c1e78a7a22085bf08d06f38fb5f72de1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -21,6 +21,11 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+/**
+ * Extension for bowtie 1
+ *
+ * Based on version 1.1.1
+ */
class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = null
@@ -53,6 +58,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var strata: Boolean = config("strata", default = false)
var maqerr: Option[Int] = config("maqerr")
+ /** return commandline to execute */
def cmdLine = {
required(executable) +
optional("--threads", nCoresRequest) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
index b6e496401257e9a259588f9092cfa089d608f980..2263b09db70b40902a802b9fbf315a6a6f317381 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
@@ -20,6 +20,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/**
+ * Extension for GNU cat
+ */
class Cat(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
var input: List[File] = Nil
@@ -29,10 +32,21 @@ class Cat(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "cat")
+ /** return commandline to execute */
def cmdLine = required(executable) + repeat(input) + " > " + required(output)
}
+/**
+ * Object for constructors for cat
+ */
object Cat {
+ /**
+ * Basis constructor
+ * @param root root object for config
+ * @param input list of files to use
+ * @param output output File
+ * @return
+ */
def apply(root: Configurable, input: List[File], output: File): Cat = {
val cat = new Cat(root)
cat.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index fc90139f8db4dba65da7e7c90df8988f68bb87e7..10aeca2920d79ccff132f6b1e86e6dc6b9e02818 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -24,6 +24,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.mutable
import scala.io.Source
+/**
+ * Extension for cutadept
+ * Based on version 1.5
+ */
class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
@Input(doc = "Input fastq file")
var fastq_input: File = _
@@ -39,17 +43,15 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
override val versionRegex = """(.*)""".r
var default_clip_mode: String = config("default_clip_mode", default = "3")
- var opt_adapter: Set[String] = Set()
- if (config.contains("adapter")) for (adapter <- config("adapter").asList) opt_adapter += adapter.toString
- var opt_anywhere: Set[String] = Set()
- if (config.contains("anywhere")) for (adapter <- config("anywhere").asList) opt_anywhere += adapter.toString
- var opt_front: Set[String] = Set()
- if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
+ var opt_adapter: Set[String] = config("adapter", default = Nil)
+ var opt_anywhere: Set[String] = config("anywhere", default = Nil)
+ var opt_front: Set[String] = config("front", default = Nil)
var opt_discard: Boolean = config("discard", default = false)
var opt_minimum_length: Int = config("minimum_length", 1)
var opt_maximum_length: Option[Int] = config("maximum_length")
+ /** return commandline to execute */
def cmdLine = required(executable) +
// options
repeat("-a", opt_adapter) +
@@ -63,6 +65,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
required("--output", fastq_output) +
" > " + required(stats_output)
+ /** Output summary stats */
def summaryStats: Map[String, Any] = {
val trimR = """.*Trimmed reads: *(\d*) .*""".r
val tooShortR = """.*Too short reads: *(\d*) .*""".r
@@ -89,6 +92,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
)
}
+ /** Merges values that can be merged for the summary */
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
(v1, v2) match {
case (v1: Int, v2: Int) => v1 + v2
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 05867d694490ebe64f6d48588f72d4288227e904..2b599ffe28587c40b2b760c06ee910f1b51c0848 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -22,6 +22,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
+/**
+ * Extension for fastqc
+ * Based on version 0.10.1 and 0.11.2
+ */
class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
@@ -48,6 +52,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
override val defaultThreads = 4
+ /** Sets contaminants and adapters when not yet set */
override def beforeGraph {
this.preProcesExecutable
@@ -59,8 +64,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
// otherwise, use default contaminants file (depending on FastQC version)
case None =>
val defaultContams = getVersion match {
- case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
- case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+ case Some("v0.11.2") => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+ case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
}
config("contaminants", default = defaultContams)
}
@@ -71,13 +76,14 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
// otherwise, check if adapters are already present (depending on FastQC version)
case None =>
val defaultAdapters = getVersion match {
- case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
- case _ => None
+ case Some("v0.11.2") => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+ case _ => None
}
defaultAdapters.collect { case adp => config("adapters", default = adp) }
}
}
+ /** return commandline to execute */
def cmdLine = required(executable) +
optional("--java", java_exe) +
optional("--threads", threads) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
index 6925a963f846c996baffac1ae0cea588cf2f7e79..d90a17b348d91bd474e90dcd91c7f58af77c31ad 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
@@ -21,6 +21,9 @@ import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
+/**
+ * This class can execute ln as InProcessFunction or used to only generate the ln command
+ */
class Ln(val root: Configurable) extends InProcessFunction with Configurable {
this.analysisName = getClass.getSimpleName
@@ -35,12 +38,14 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
var relative: Boolean = true
+ /** Generate out file for job */
override def freezeFieldValues(): Unit = {
val outLog: String = ".%s.%s.out".format(out.getName, analysisName)
jobOutputFile = new File(out.getAbsoluteFile.getParentFile, outLog)
super.freezeFieldValues()
}
+ /** return commandline to execute */
lazy val cmd: String = {
lazy val inCanonical: String = {
// need to remove "/~" to correctly expand path with tilde
@@ -113,7 +118,17 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
}
}
+/** Object for constructors for ln */
object Ln {
+ /**
+ * Basis constructor
+ * @param root root object for config
+ * @param input list of files to use
+ * @param output output File
+ * @param relative make reletive links (default true)
+ * @return
+ */
+
def apply(root: Configurable, input: File, output: File, relative: Boolean = true): Ln = {
val ln = new Ln(root)
ln.in = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
index a266719a58af2345badfd5501261cb4473e9fa5f..fa177b8fe4cd52cfee1307dbb4e9aeeb5ded4e08 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
@@ -23,6 +23,7 @@ import argonaut._, Argonaut._
import scalaz._, Scalaz._
import scala.io.Source
+/** Extension for md5sum */
class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input")
var input: File = _
@@ -32,17 +33,13 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "md5sum")
+ /** return commandline to execute */
def cmdLine = required(executable) + required(input) + " > " + required(output)
-
- def getSummary: Json = {
- val data = Source.fromFile(output).mkString.split(" ")
- return ("path" := output.getAbsolutePath) ->:
- ("md5sum" := data(0)) ->:
- jEmptyObject
- }
}
+/** Object for constructors for md5sum */
object Md5sum {
+ /** Makes md5sum with md5 file in given dir */
def apply(root: Configurable, fastqfile: File, outDir: File): Md5sum = {
val md5sum = new Md5sum(root)
md5sum.input = fastqfile
@@ -50,6 +47,7 @@ object Md5sum {
return md5sum
}
+ /** Makes md5sum with md5 file in same dir as input file */
def apply(root: Configurable, file: File): Md5sum = {
val md5sum = new Md5sum(root)
md5sum.input = file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
index 03f76abd6162f5759fb772158a5f1dc941012b1c..6756c5eafc7ab5b9a3ba1fd60fc89154bc0aa0df 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for pbzip2 */
class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Zipped file")
var input: File = _
@@ -39,6 +40,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
if (!memory.isEmpty) memory = Option(memory.get * threads)
}
+ /** return commandline to execute */
def cmdLine = required(executable) +
conditional(decomrpess, "-d") +
conditional(!decomrpess, "-z") +
@@ -48,7 +50,9 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
required(input)
}
+/** Object for constructors for Pbzip2 */
object Pbzip2 {
+ /** Default constructor */
def apply(root: Configurable, input: File, output: File): Pbzip2 = {
val pbzip2 = new Pbzip2(root)
pbzip2.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
index ebfaac812bbedec10a14d0daad609d54469f9c03..cf088cb29fa57d66b1fb9fe24b247054e0ae2edc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
@@ -28,6 +28,11 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
executable = config("exe", default = "python", submodule = "python")
protected var python_script_name: String = _
+
+ /**
+ * checks if script already exist in jar otherwise try to fetch from the jar
+ * @param script name / location of script
+ */
def setPythonScript(script: String) {
python_script = new File(script)
if (!python_script.exists()) {
@@ -36,6 +41,12 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
python_script_name = script
}
}
+
+ /**
+ * Set and extract python script from jar file
+ * @param script name of script in jar
+ * @param subpackage location of script in jar
+ */
def setPythonScript(script: String, subpackage: String) {
python_script_name = script
python_script = new File(".queue/tmp/" + subpackage + python_script_name)
@@ -46,6 +57,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
os.close()
}
+ /** return basic command to prefix the complete command with */
def getPythonCommand(): String = {
required(executable) + required(python_script)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 12a36ad800a36d78d0237cc1358a1891e3a66675..ff7b56110c342c32b30e0af7c67cfc3118240eb5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -19,7 +19,12 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
+import scalaz.std.boolean.option
+/**
+ * extension for raxml
+ * based on version 8.1.3
+ */
class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 1
@@ -50,49 +55,51 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
@Argument(doc = "Output directory", required = true)
var w: File = null
- var noBfgs: Boolean = config("no_bfgs", default = false)
-
@Input(required = false)
- var t: File = _
+ var t: Option[File] = _
@Input(required = false)
- var z: File = _
+ var z: Option[File] = _
@Output(doc = "Output files", required = false)
private var out: List[File] = Nil
+ var noBfgs: Boolean = config("no_bfgs", default = false)
+
var executableNonThreads: String = config("exe", default = "raxmlHPC")
var executableThreads: Option[String] = config("exe_pthreads")
+ /** Sets correct output files to job */
override def beforeGraph {
require(w != null)
if (threads == 0) threads = getThreads(defaultThreads)
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
super.beforeGraph
- out +:= getInfoFile
+ out :::= List(Some(getInfoFile), getBestTreeFile, getBootstrapFile, getBipartitionsFile).flatten
f match {
- case "d" if b.isEmpty => {
- out +:= getBestTreeFile
- for (t <- 0 until N.getOrElse(1)) {
- out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
- out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
- out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
- }
- }
- case "d" if b.isDefined => out +:= getBootstrapFile
- case "b" => {
- out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
- out +:= new File(w, "RAxML_bipartitions." + n)
+ case "d" if b.isEmpty => for (t <- 0 until N.getOrElse(1)) {
+ out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
+ out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
+ out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
}
- case _ =>
+ case "b" => out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
+ case _ =>
}
}
- def getBestTreeFile: File = new File(w, "RAxML_bestTree." + n)
- def getBootstrapFile: File = new File(w, "RAxML_bootstrap." + n)
- def getBipartitionsFile: File = new File(w, "RAxML_bipartitions." + n)
- def getInfoFile: File = new File(w, "RAxML_info." + n)
+ /** Returns bestTree file */
+ def getBestTreeFile = option(f == "d" && b.isEmpty, new File(w, "RAxML_bestTree." + n))
+
+ /** Returns bootstrap file */
+ def getBootstrapFile = option(f == "d" && b.isDefined, new File(w, "RAxML_bootstrap." + n))
+
+ /** Returns bipartitions file */
+ def getBipartitionsFile = option(f == "b", new File(w, "RAxML_bipartitions." + n))
+
+ /** Returns info file */
+ def getInfoFile = new File(w, "RAxML_info." + n)
+ /** return commandline to execute */
def cmdLine = required(executable) +
required("-m", m) +
required("-s", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index 454572dab193e18d10056a516d41555e75bc87f6..df69543eaa4b4b4667786dc6b2008a85b28faf5e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -21,6 +21,11 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+/**
+ * Extension for gubbins
+ * See; https://github.com/sanger-pathogens/gubbins
+ * No version known
+ */
class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
@@ -47,6 +52,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var verbose: Boolean = config("verbose", default = false)
var noCleanup: Boolean = config("no_cleanup", default = false)
+ /** Set correct output files */
override def beforeGraph: Unit = {
super.beforeGraph
require(outputDirectory != null)
@@ -63,6 +69,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix.getOrElse("gubbins") + t)
}
+ /** Return command to execute */
def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
optional("--outgroup", outgroup) +
optional("--starting_tree", startingTree) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
index 44cb16ec0f2b1d8077b471fbd0f313d9ca9319ca..91eb8458df0cbd820b3d5bb7ecec9613882d2cf4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
@@ -23,6 +23,7 @@ import argonaut._, Argonaut._
import scalaz._, Scalaz._
import scala.io.Source
+/** Extension for sha1sum */
class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file")
var input: File = _
@@ -32,21 +33,16 @@ class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "sha1sum")
+ /** Set correct output files */
def cmdLine = required(executable) + required(input) + " > " + required(output)
-
- def getSummary: Json = {
- val data = Source.fromFile(output).mkString.split(" ")
- return ("path" := output.getAbsolutePath) ->:
- ("sha1sum" := data(0)) ->:
- jEmptyObject
- }
}
object Sha1sum {
- def apply(root: Configurable, fastqfile: File, outDir: String): Sha1sum = {
+ /** Create default sha1sum */
+ def apply(root: Configurable, input: File, outDir: File): Sha1sum = {
val sha1sum = new Sha1sum(root)
- sha1sum.input = fastqfile
- sha1sum.output = new File(outDir + fastqfile.getName + ".sha1")
+ sha1sum.input = input
+ sha1sum.output = new File(outDir, input.getName + ".sha1")
return sha1sum
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index fae8c5802c3979af507421df955a91400d21923d..2ff9e6947bc7366180aaa6236b78768eadcad039 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -25,6 +25,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.mutable
import scala.io.Source
+/**
+ * Extension for sickle
+ * Based on version 1.33
+ */
class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
@Input(doc = "R1 input")
var input_R1: File = _
@@ -57,10 +61,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
override val versionRegex = """sickle version (.*)""".r
override def versionCommand = executable + " --version"
+ /** Sets qualityType is still empty */
override def beforeGraph {
if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
}
+ /** Return command to execute */
def cmdLine = {
var cmd: String = required(executable)
if (input_R2 != null) {
@@ -81,6 +87,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
" > " + required(output_stats)
}
+ /** returns stats map for summary */
def summaryStats: Map[String, Any] = {
val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
@@ -108,6 +115,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
stats.toMap
}
+ /** Merge stats incase of chunking */
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
(v1, v2) match {
case (v1: Int, v2: Int) => v1 + v2
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index bb412a8fbc23a41bf64b905e349b4cc0787c6145..a9cbbd6689ea26b7ab799131df6a858e35e5c571 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+/** Extension for stampy */
class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "FastQ file R1", shortName = "R1")
var R1: File = _
@@ -68,12 +69,14 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --help"
+ /** Sets readgroup when not set yet */
override def beforeGraph: Unit = {
super.beforeGraph
require(readgroup != null)
}
- def cmdLine: String = {
+ /** Returns command to execute */
+ def cmdLine = {
var cmd: String = required(executable) +
optional("-t", nCoresRequest) +
conditional(solexa, "--solexa") +
@@ -99,6 +102,6 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
" -h " + required(hash) +
" -o " + required(output) +
" -M " + required(R1) + optional(R2)
- return cmd
+ cmd
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 9404a895006398d7cd3cca35b3259846af1d6aa0..57f94660b47088756cc589bd8446cba389971106 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+/**
+ * Extension for STAR
+ */
class Star(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "The reference file for the bam files.", required = false)
var reference: File = new File(config("reference"))
@@ -62,6 +65,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultVmem = "6G"
override val defaultThreads = 8
+ /** Sets output files for the graph */
override def beforeGraph() {
if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
@@ -77,7 +81,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
}
- def cmdLine: String = {
+ /** Returns command to execute */
+ def cmdLine = {
var cmd: String = required("cd", outputDir) + "&&" + required(executable)
if (runmode != null && runmode == "genomeGenerate") { // Create index
cmd += required("--runMode", runmode) +
@@ -91,11 +96,22 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
optional("--outFileNamePrefix", outFileNamePrefix)
if (sjdbOverhang > 0) cmd += optional("--sjdbOverhang", sjdbOverhang)
- return cmd
+ cmd
}
}
object Star {
+ /**
+ * Create default star
+ * @param configurable root object
+ * @param R1 R1 fastq file
+ * @param R2 R2 fastq file
+ * @param outputDir Outputdir for Star
+ * @param isIntermediate
+ * @param deps Deps to add to wait on run
+ * @return Return Star
+ *
+ */
def apply(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
val star = new Star(configurable)
star.R1 = R1
@@ -107,7 +123,22 @@ object Star {
return star
}
- def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): (File, List[Star]) = {
+ /**
+ * returns Star with 2pass star method
+ * @param configurable root object
+ * @param R1 R1 fastq file
+ * @param R2 R2 fastq file
+ * @param outputDir Outputdir for Star
+ * @param isIntermediate
+ * @param deps Deps to add to wait on run
+ * @return Return Star
+ */
+ def _2pass(configurable: Configurable,
+ R1: File,
+ R2: File,
+ outputDir: File,
+ isIntermediate: Boolean = false,
+ deps: List[File] = Nil): (File, List[Star]) = {
val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
starCommand_pass1.isIntermediate = isIntermediate
starCommand_pass1.deps = deps
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index ce86a1ed9bd1e8d1afa04867887be2f21cf6231b..169c3274c9d68948db70111ae0aa3cf9091f0a96 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+/**
+ * Extension for TopHad
+ */
class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "FastQ file R1", shortName = "R1")
var R1: File = _
@@ -70,11 +73,10 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
}
def cmdLine: String = {
- var cmd: String = required(executable) +
+ required(executable) +
optional("-p", nCoresRequest) +
"--no-convert-bam" +
required(bowtie_index) +
required(R1) + optional(R2)
- return cmd
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 1ece3133f711a4b261a6c7586d76567da10d15d7..7e6c53fb7fda7a693334920af1954f9947294d5f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
+ * Extension for VariantEffectPredictor
* Created by ahbbollen on 15-1-15.
*/
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
@@ -134,6 +135,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
}
}
+ /** Returns command to execute */
def cmdLine = required(executable) +
required(vep_script) +
required("-i", input) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
index 9c98893c9a4f22216cbcc57041bf7ca65b50be7e..5fcea15723224c7d3da5e3c78193d5ad4de32f75 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
@@ -27,6 +27,7 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
var clip: Boolean = config("clip", default = false)
var unc: Boolean = config("unc", default = false)
+ /** Returns command to execute */
def cmdLine = required(executable) +
optional("-blockSize=", blockSize, spaceSeparated = false) +
optional("-itemsPerSlot=", itemsPerSlot, spaceSeparated = false) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
index 7b1aeb0770be29991d791b07db5b937372d9e565..e8fa8cd7cbddf8714975386fb0d7a426c24144bc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
+/** Extension for zcat */
class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Zipped file")
var input: File = _
@@ -29,10 +30,12 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "zcat")
+ /** Returns command to execute */
def cmdLine = required(executable) + required(input) + " > " + required(output)
}
object Zcat {
+ /** Returns a default zcat */
def apply(root: Configurable, input: File, output: File): Zcat = {
val zcat = new Zcat(root)
zcat.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
index cf7f16e381093eb0e4a547434b4e119936cd44b6..d9aa1dd948077509e73494b09046f7cd377f3398 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+/** General abstract class for bedtools extensions */
abstract class Bedtools extends BiopetCommandLineFunction {
override def subPath = "bedtools" :: super.subPath
executable = config("exe", default = "bedtools", submodule = "bedtools")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index 37266ccb1155726772fe2cca51280b4dbd273f5c..73ddfc8037cd1c44b865ebd6afd63aa202cb6872 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
+/** Extension for bedtools coverage */
class BedtoolsCoverage(val root: Configurable) extends Bedtools {
@Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = _
@@ -44,6 +45,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
+ /** Returns command to execute */
def cmdLine = required(executable) + required("coverage") +
required(inputTag, input) +
required("-b", intersectFile) +
@@ -54,6 +56,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
}
object BedtoolsCoverage {
+ /** Returns defaul bedtools coverage */
def apply(root: Configurable, input: File, intersect: File, output: File,
depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
val bedtoolsCoverage = new BedtoolsCoverage(root)
@@ -63,6 +66,6 @@ object BedtoolsCoverage {
bedtoolsCoverage.depth = depth
bedtoolsCoverage.sameStrand = sameStrand
bedtoolsCoverage.diffStrand = diffStrand
- return bedtoolsCoverage
+ bedtoolsCoverage
}
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
index 19071be64a67068f7c734245cffc68008b891a3e..8465efca792455dbeaeea1a0c74ef29fcc727380 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
+/** Extension for bedtools intersect */
class BedtoolsIntersect(val root: Configurable) extends Bedtools {
@Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = _
@@ -41,6 +42,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
+ /** Returns command to execute */
def cmdLine = required(executable) + required("intersect") +
required(inputTag, input) +
required("-b", intersectFile) +
@@ -50,6 +52,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
}
object BedtoolsIntersect {
+ /** Returns default bedtools intersect */
def apply(root: Configurable, input: File, intersect: File, output: File,
minOverlap: Double = 0, count: Boolean = false): BedtoolsIntersect = {
val bedtoolsIntersect = new BedtoolsIntersect(root)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
index 3e0ffc8011a1669b3205157cce5bde5d3d5053f1..35299b3ef40682a5841ef3a1f0bf325b41d10c12 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
+ * General bwa extension
+ *
* Created by pjvan_thof on 1/16/15.
*/
abstract class Bwa extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index 3298702fcfd5cd98e1eaf0bae8f6b059d353d2c9..945411d77b32364002d278df27d0154c3fed47ef 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -6,6 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
+ * Extension for bwa aln
+ *
+ * Based on version 0.7.12-r1039
+ *
* Created by pjvan_thof on 1/16/15.
*/
class BwaAln(val root: Configurable) extends Bwa {
@@ -44,6 +48,7 @@ class BwaAln(val root: Configurable) extends Bwa {
override val defaultVmem = "5G"
override val defaultThreads = 8
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("aln") +
optional("-n", n) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 731cdc2787edebf111cdc703393ad40937cbb032..3eb1cd45055183ad4174de09bc2f457f08c93c3c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -22,6 +22,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+/**
+ * Extension for bwa mem
+ *
+ * Based on version 0.7.12-r1039
+ */
class BwaMem(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index 255811561e732b229b1417c95d866fad4694c0c9..7e190e59309ae3901e90aa34c6e54cd101be933b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -10,7 +10,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
*
* based on executable version 0.7.10-r789
*
- * @param root Configurable
*/
class BwaSampe(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index 8bbf918474e21d2e2837ce01d5bc4490e13bd087..b302425d9a1c7e72fdea9c69fa8417f0b7885c6c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -6,7 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
- * Created by pjvan_thof on 1/16/15.
+ * BWA samse wrapper
+ *
+ * based on executable version 0.7.10-r789
+ *
*/
class BwaSamse(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file", required = true)
@@ -24,6 +27,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var n: Option[Int] = config("n")
var r: String = _
+ /** Returns command to execute */
def cmdLine = required(executable) +
required("samse") +
optional("-n", n) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
index aff6ee16cdfbf1a77529d079bc1789c9ffcc494b..c232c03f8674c1eb600c53dd689ac2055df6e16b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
@@ -6,6 +6,7 @@ package nl.lumc.sasc.biopet.extensions.igvtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+/** General igvtools extension */
abstract class IGVTools extends BiopetCommandLineFunction {
executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
override def versionCommand = executable + " version"
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index 37589c5d2b32caf210cec84204bb81e1f2fbd030..fc9b404c09bde8db694fc0cdda1c676ecbfa601e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -61,6 +61,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
throw new IllegalArgumentException("TDF file should have a .tdf file-extension"))
}
+ /** Returns command to execute */
def cmdLine = {
required(executable) +
required("count") +
@@ -81,10 +82,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
required(genomeChromSizes)
}
- /**
- * This part should never fail, these values are set within this wrapper
- *
- */
+ /** This part should never fail, these values are set within this wrapper */
private def outputArg: String = {
(tdf, wig) match {
case (None, None) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
index 5c52970ed8cc0c049ef236f571acedbb8a4610dd..8163d47aa4228b691d1300ec80d280a174b33052 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.macs2
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
+ * General igvtools extension
+ *
* Created by sajvanderzeeuw on 12/19/14.
*/
abstract class Macs2 extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index 6c572f2292bf3813b254d36370f759cb3e225b84..fbb003a3a9265ee08321ccdeec9723c1a46db7da 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -5,6 +5,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+/** Extension for macs2*/
class Macs2CallPeak(val root: Configurable) extends Macs2 {
@Input(doc = "Treatment input", required = true)
var treatment: File = _
@@ -56,6 +57,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var broadcutoff: Option[Int] = config("broadcutoff")
var callsummits: Boolean = config("callsummits", default = false)
+ /** Sets output files */
override def beforeGraph: Unit = {
if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
@@ -67,6 +69,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
output_gapped = new File(outputdir + name.get + ".gappedPeak")
}
+ /** Returns command to execute */
def cmdLine = {
required(executable) + required("callpeak") +
required("--treatment", treatment) + /* Treatment sample */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
index c980492349c480976e7240db0e3f83f884306b4b..232cbc24123983bc46f7c51f98284be10bb6f2a8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard AddOrReplaceReadGroups */
class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.AddOrReplaceReadGroups"
@@ -61,6 +62,7 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
@Argument(doc = "RGPI", required = false)
var RGPI: Option[Int] = _
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -77,6 +79,7 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
}
object AddOrReplaceReadGroups {
+ /** Returns default AddOrReplaceReadGroups */
def apply(root: Configurable, input: File, output: File, sortOrder: String = null): AddOrReplaceReadGroups = {
val addOrReplaceReadGroups = new AddOrReplaceReadGroups(root)
addOrReplaceReadGroups.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index 4aa970f636ddbbb7216abce5d96ebbbebc8a7598..974fd43c5ad00fd0c8fe15955c7c9379417d2595 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard CalculateHsMetrics */
class CalculateHsMetrics(val root: Configurable) extends Picard {
javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
@@ -46,6 +47,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
@Argument(doc = "BAIT_SET_NAME", required = false)
var baitSetName: String = _
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -58,6 +60,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
}
object CalculateHsMetrics {
+ /** Returns default CalculateHsMetrics */
def apply(root: Configurable, input: File, baitIntervals: File, targetIntervals: File, outputDir: File): CalculateHsMetrics = {
val calculateHsMetrics = new CalculateHsMetrics(root)
calculateHsMetrics.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 53b109b8c4fc549924b8f494993f661ec09598ad..692a260f4c3d238902e2cac34f7885a9dcae6c9f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard CollectAlignmentSummaryMetrics */
class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
@@ -50,6 +51,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
@Argument(doc = "STOP_AFTER", required = false)
var stopAfter: Option[Long] = config("stopAfter")
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -63,6 +65,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
def summaryFiles: Map[String, File] = Map()
+ /** Returns stats for summary */
def summaryStats: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
@@ -79,6 +82,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
}
object CollectAlignmentSummaryMetrics {
+ /** Returns default CollectAlignmentSummaryMetrics */
def apply(root: Configurable, input: File, outputDir: File): CollectAlignmentSummaryMetrics = {
val collectAlignmentSummaryMetrics = new CollectAlignmentSummaryMetrics(root)
collectAlignmentSummaryMetrics.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 86198d2a344489a62b546f5d9c0dd4a8234c929a..f93dc4aa77241dabfee7c0703536fda9cb6afa2c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard CollectGcBiasMetrics */
class CollectGcBiasMetrics(val root: Configurable) extends Picard {
javaMainClass = "picard.analysis.CollectGcBiasMetrics"
@@ -51,9 +52,9 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
override def beforeGraph {
if (outputChart == null) outputChart = new File(output + ".pdf")
- //require(reference.exists)
}
+ /** Returns command to execute */
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -67,6 +68,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
}
object CollectGcBiasMetrics {
+ /** Returns default CollectGcBiasMetrics */
def apply(root: Configurable, input: File, outputDir: File): CollectGcBiasMetrics = {
val collectGcBiasMetrics = new CollectGcBiasMetrics(root)
collectGcBiasMetrics.input :+= input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 867e6f6802493a9dfdcf767ef44bde8d8b61abfb..b4dcba1a5aa3a44b2046643341d3124d5bc2e3cc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -22,6 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import scala.collection.immutable.Nil
+/** Extension for picard CollectInsertSizeMetrics */
class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
@@ -57,10 +58,9 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
override def beforeGraph {
outputHistogram = new File(output + ".pdf")
- //if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
- //require(reference.exists)
}
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -72,8 +72,10 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
optional("HISTOGRAM_WIDTH=", histogramWidth, spaceSeparated = false) +
conditional(assumeSorted, "ASSUME_SORTED=TRUE")
+ /** Returns files for summary */
def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
+ /** Returns stats for summary */
def summaryStats: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
(for (i <- 0 to header.size if i < content.head.size)
@@ -82,6 +84,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
}
object CollectInsertSizeMetrics {
+ /** Returns default CollectInsertSizeMetrics */
def apply(root: Configurable, input: File, outputDir: File): CollectInsertSizeMetrics = {
val collectInsertSizeMetrics = new CollectInsertSizeMetrics(root)
collectInsertSizeMetrics.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index fd0f28e73e1149d57d000a9082132c909c00f522..1511fa93f46870bb8e89505c50bc2ecd86fa0c22 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard MarkDuplicates */
class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.sam.MarkDuplicates"
@@ -76,6 +77,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
+ /** Returns command to execute */
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -93,8 +95,10 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
optional("READ_NAME_REGEX=", readNameRegex, spaceSeparated = false) +
optional("OPTICAL_DUPLICATE_PIXEL_DISTANCE=", opticalDuplicatePixelDistance, spaceSeparated = false)
+ /** Returns files for summary */
def summaryFiles: Map[String, File] = Map()
+ /** Returns stats for summary */
def summaryStats: Map[String, Any] = {
val (header, content) = Picard.getMetrics(outputMetrics)
@@ -110,19 +114,12 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
}
}
object MarkDuplicates {
- def apply(root: Configurable, input: List[File], outputDir: String): MarkDuplicates = {
- val markDuplicates = new MarkDuplicates(root)
- markDuplicates.input = input
- markDuplicates.output = new File(outputDir, input.head.getName.stripSuffix(".bam") + ".dedup.bam")
- markDuplicates.outputMetrics = new File(outputDir, input.head.getName.stripSuffix(".bam") + ".dedup.metrics")
- return markDuplicates
- }
-
+ /** Returns default MarkDuplicates */
def apply(root: Configurable, input: List[File], output: File): MarkDuplicates = {
val markDuplicates = new MarkDuplicates(root)
markDuplicates.input = input
markDuplicates.output = output
markDuplicates.outputMetrics = new File(output.getParent, output.getName.stripSuffix(".bam") + ".metrics")
- return markDuplicates
+ markDuplicates
}
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index 8feaf782ac57aba5a6779e515fe2c6ce452f5871..ef3f358ab1598680a5f7b1fcb690232dd020bbe6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard MergeSamFiles */
class MergeSamFiles(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.MergeSamFiles"
@@ -43,6 +44,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
@Argument(doc = "COMMENT", required = false)
var comment: Option[String] = config("comment")
+ /** Returns command to execute */
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -53,12 +55,13 @@ class MergeSamFiles(val root: Configurable) extends Picard {
}
object MergeSamFiles {
+ /** Returns default MergeSamFiles */
def apply(root: Configurable, input: List[File], outputDir: File, 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
+ mergeSamFiles
}
}
\ No newline at end of file
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 12d9f05f6998fcac6462c3b65a2695a8471a73eb..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
@@ -22,9 +22,16 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument }
import scala.io.Source
+/**
+ * General picard extension
+ *
+ * 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
+ if (config.contains("picard_jar")) jarFile = config("picard_jar")
+
@Argument(doc = "VERBOSITY", required = false)
var verbosity: Option[String] = config("verbosity")
@@ -46,10 +53,12 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
@Argument(doc = "CREATE_MD5_FILE", required = false)
var createMd5: Boolean = config("createmd5", default = false)
- //FIXME: picard version
- // override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
- // override val versionRegex = """Version: (.*)""".r
- // override val versionExitcode = List(0, 1)
+ override def versionCommand = {
+ if (jarFile != null) executable + " -cp " + jarFile + " " + javaMainClass + " -h"
+ else null
+ }
+ override val versionRegex = """Version: (.*)""".r
+ override val versionExitcode = List(0, 1)
override val defaultVmem = "8G"
memoryLimit = Option(3.0)
@@ -66,6 +75,11 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
}
object Picard {
+ /**
+ * This function parse a metrics file in separated values
+ * @param file input metrics file
+ * @return (header, content)
+ */
def getMetrics(file: File) = {
val lines = Source.fromFile(file).getLines().toArray
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index c3a4226d01cbbb0680a22e3e0c6ccaeb68b7398c..96bfdf4223851b83d137a066cfbf3df8d222659e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard SamToFastq */
class SamToFastq(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SamToFastq"
@@ -70,6 +71,7 @@ class SamToFastq(val root: Configurable) extends Picard {
@Argument(doc = "includeNonPrimaryAlignments", required = false)
var includeNonPrimaryAlignments: Boolean = config("includeNonPrimaryAlignments", default = false)
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("FASTQ=", fastqR1, spaceSeparated = false) +
@@ -90,11 +92,12 @@ class SamToFastq(val root: Configurable) extends Picard {
}
object SamToFastq {
+ /** Returns default SamToFastq */
def apply(root: Configurable, input: File, fastqR1: File, fastqR2: File = null): SamToFastq = {
val samToFastq = new SamToFastq(root)
samToFastq.input = input
samToFastq.fastqR1 = fastqR1
samToFastq.fastqR2 = fastqR2
- return samToFastq
+ samToFastq
}
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index ef7ec250d5de2bd88c36e48af157ae29bce0a3b0..8d2946291928f4019c52e1cdc7b6bf52c00df89a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+/** Extension for picard SortSam */
class SortSam(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SortSam"
@@ -39,6 +40,7 @@ class SortSam(val root: Configurable) extends Picard {
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
+ /** Returns command to execute */
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
@@ -46,6 +48,7 @@ class SortSam(val root: Configurable) extends Picard {
}
object SortSam {
+ /** Returns default SortSam */
def apply(root: Configurable, input: File, output: File, sortOrder: String = null): SortSam = {
val sortSam = new SortSam(root)
sortSam.input = input
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 2de91382d2a5231f4c112ed1915dd34559a11cc5..a90c569037ce707ccc420664255dd13a6cbd9e5a 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: List[File] = Nil
@@ -47,6 +48,8 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
conditional(u, "-u")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + repeat(input)
+
+ /** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
}
@@ -69,4 +72,4 @@ object SamtoolsMpileup {
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".mpileup"
-}
\ No newline at end of file
+}
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)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
index b3233ecfecbf070a36cf5db6aaf73f0a8cf4aa07..a75a1424610ba1a537ea9c5011785b248d9f8839 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
@@ -19,46 +19,63 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript, BiopetQSc
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
+/** Template for a multisample pipeline */
class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
+ /** Location of summary file */
def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
+ /** File to add to the summary */
def summaryFiles: Map[String, File] = Map()
+ /** Pipeline settings to add to the summary */
def summarySettings: Map[String, Any] = Map()
+ /** Function to make a sample */
def makeSample(id: String) = new Sample(id)
+ /** This class will contain jobs and libraries for a sample */
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ /** Sample specific files for summary */
def summaryFiles: Map[String, File] = Map()
+ /** Sample specific stats for summary */
def summaryStats: Map[String, Any] = Map()
+ /** Function to make a library */
def makeLibrary(id: String) = new Library(id)
+
+ /** This class will contain all jobs for a library */
class Library(libId: String) extends AbstractLibrary(libId) {
+ /** Library specific files for summary */
def summaryFiles: Map[String, File] = Map()
+ /** Library specific stats for summary */
def summaryStats: Map[String, Any] = Map()
+ /** Method to add library jobs */
protected def addJobs(): Unit = {
- // Library jobs
}
}
+ /** Method to add sample jobs */
protected def addJobs(): Unit = {
- // Sample jobs
}
}
+ /** Method where multisample jobs are added */
def addMultiSampleJobs(): Unit = {
}
+ /** This is executed before the script starts */
def init(): Unit = {
}
+ /** Method where jobs must be added */
def biopetScript() {
}
}
+/** Object to let to generate a main method */
object MultisamplePipelineTemplate extends PipelineCommand
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
index 6278ab6f87cdf9c23ed3b8431642117d82ad8fc9..d4998770e07bfd19a26746e01a49adb29e7cb962 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
@@ -20,14 +20,18 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._
+/** Template for a pipeline */
class PipelineTemplate(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
+ /** This is executed before the script starts */
def init() {
}
+ /** Method where jobs must be added */
def biopetScript() {
}
}
+/** Object to let to generate a main method */
object PipelineTemplate extends PipelineCommand
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 4e1d50fbcd96b45aa067ce845a2dc501eff2e4a7..446bdb29c433fd8c45313caf0bb770c494deecac 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
@@ -164,14 +164,11 @@ object Seqstat extends ToolCommand {
case class ReadStat(qual: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer(),
nuc: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer.fill('T'.toInt + 1)(0),
- var withN: Long,
+ var withN: Long = 0L,
lengths: mutable.ArrayBuffer[Int] = mutable.ArrayBuffer())
val baseStats: mutable.ArrayBuffer[BaseStat] = mutable.ArrayBuffer()
- val readStats: ReadStat = new ReadStat(mutable.ArrayBuffer(),
- mutable.ArrayBuffer.fill('T'.toInt + 1)(0),
- 0L,
- mutable.ArrayBuffer())
+ val readStats: ReadStat = new ReadStat()
/**
* Compute the quality metric per read
@@ -194,6 +191,9 @@ object Seqstat extends ToolCommand {
val readQual = record.getBaseQualityString
val readNucleotides = record.getReadString
+ if (record.length >= readStats.lengths.size) // Extends array when length not yet possible
+ (0 to (record.length - readStats.lengths.size)).foreach(_ => readStats.lengths.append(0))
+
readStats.lengths(record.length) += 1
for (t <- 0 until record.length()) {
@@ -211,10 +211,7 @@ object Seqstat extends ToolCommand {
readStats.qual ++= mutable.ArrayBuffer.fill(avgQual - readStats.qual.length + 1)(0)
}
readStats.qual(avgQual) += 1
- readStats.withN += {
- if (readNucleotides.contains("N")) 1L
- else 0L
- }
+ if (readNucleotides.contains("N")) readStats.withN += 1L
}
/**
@@ -278,7 +275,7 @@ object Seqstat extends ToolCommand {
}
for (pos <- 0 until readStats.qual.length) {
- var key: Int = pos - phredEncoding.id
+ val key: Int = pos - phredEncoding.id
if (key > 0) {
// count till the max of baseHistogram.length
for (histokey <- 0 until key + 1) {
@@ -319,7 +316,7 @@ object Seqstat extends ToolCommand {
),
("stats", Map(
("bases", Map(
- ("num_n", nucleotideHistoMap('N')),
+ ("num_n", nucleotideHistoMap.getOrElse('N', 0)),
("num_total", nucleotideHistoMap.values.sum),
("num_qual_gte", baseQualHistoMap.toMap),
("nucleotides", nucleotideHistoMap.toMap)
@@ -335,9 +332,6 @@ object Seqstat extends ToolCommand {
))
)
- val jsonReport: Json = {
- ConfigUtils.mapToJson(report)
- }
- println(jsonReport.spaces2)
+ println(ConfigUtils.mapToJson(report).spaces2)
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
index 9d6e983a4f90120f5f2df6d31a489e29c560bb5a..7f704c12aae8d78a73e42ca81323f69a940bda0d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
@@ -32,6 +32,13 @@ object VcfUtils {
alleles(longestAlleleId)
}
+ /**
+ * Method will extend a allele till a new length
+ * @param bases Allele
+ * @param newSize New size of allele
+ * @param fillWith Char to fill gap
+ * @return
+ */
def fillAllele(bases: String, newSize: Int, fillWith: Char = '-'): String = {
bases + (Array.fill[Char](newSize - bases.size)(fillWith)).mkString
}
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 876da87289b56d183d070293468dcff9bc493931..1d22bb55b9ea174c2c640b1585dc01015116bb81 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -20,7 +20,7 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.extensions.{ Ln, Star, Stampy, Bowtie }
+import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.tools.FastqSplitter
@@ -163,9 +163,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
- else chunks += (outputDir -> (
- flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
- if (paired) flexiprep.extractIfNeeded(input_R2.get, flexiprep.outputDir) else "")
+ else if (skipFlexiprep) {
+ chunks += (outputDir -> (
+ extractIfNeeded(input_R1, flexiprep.outputDir),
+ if (paired) extractIfNeeded(input_R2.get, outputDir) else "")
+ )
+ } else chunks += (outputDir -> (
+ flexiprep.outputFiles("fastq_input_R1"),
+ if (paired) flexiprep.outputFiles("fastq_input_R2") else "")
)
if (chunking) {
@@ -441,6 +446,32 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
return RG.substring(0, RG.lastIndexOf("\\t"))
}
+
+ //FIXME: This is code duplication from flexiprep, need general class to pass jobs inside a util function
+ /**
+ * Extracts file if file is compressed
+ * @param file
+ * @param runDir
+ * @return returns extracted file
+ */
+ def extractIfNeeded(file: File, runDir: File): File = {
+ if (file == null) return file
+ else if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
+ var newFile: File = swapExt(runDir, file, ".gz", "")
+ if (file.getName().endsWith(".gzip")) newFile = swapExt(runDir, file, ".gzip", "")
+ val zcatCommand = Zcat(this, file, newFile)
+ zcatCommand.isIntermediate = true
+ add(zcatCommand)
+ return newFile
+ } else if (file.getName().endsWith(".bz2")) {
+ val newFile = swapExt(runDir, file, ".bz2", "")
+ val pbzip2 = Pbzip2(this, file, newFile)
+ pbzip2.isIntermediate = true
+ add(pbzip2)
+ return newFile
+ } else return file
+ }
+
}
object Mapping extends PipelineCommand
\ No newline at end of file
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 5357811e964b4955115dbded66a6a3d3baaa0878..c95fe06035f42fd6e7b5bd64df2b76a6bef99542 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -37,18 +37,23 @@ class MappingTest extends TestNGSuite with Matchers {
val chunks = Array(1, 5, 10, 100)
val skipMarkDuplicates = Array(true, false)
val skipFlexipreps = Array(true, false)
+ val zipped = Array(true, false)
for (
aligner <- aligners;
pair <- paired;
chunk <- chunks;
skipMarkDuplicate <- skipMarkDuplicates;
- skipFlexiprep <- skipFlexipreps
- ) yield Array(aligner, pair, chunk, skipMarkDuplicate, skipFlexiprep)
+ skipFlexiprep <- skipFlexipreps;
+ zipped <- zipped
+ ) yield Array(aligner, pair, chunk, skipMarkDuplicate, skipFlexiprep, zipped)
}
@Test(dataProvider = "mappingOptions")
- def testMapping(aligner: String, paired: Boolean, chunks: Int, skipMarkDuplicate: Boolean, skipFlexiprep: Boolean) = {
+ def testMapping(aligner: String, paired: Boolean, chunks: Int,
+ skipMarkDuplicate: Boolean,
+ skipFlexiprep: Boolean,
+ zipped: Boolean) = {
val map = ConfigUtils.mergeMaps(Map("output_dir" -> MappingTest.outputDir,
"aligner" -> aligner,
"number_chunks" -> chunks,
@@ -57,15 +62,20 @@ class MappingTest extends TestNGSuite with Matchers {
), Map(MappingTest.executables.toSeq: _*))
val mapping: Mapping = initPipeline(map)
- mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
- if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq"))
+ if (zipped) {
+ mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq.gz")
+ if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq.gz"))
+ } else {
+ mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
+ if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq"))
+ }
mapping.sampleId = Some("1")
mapping.libId = Some("1")
mapping.script()
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
- mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
+ mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (!zipped || (chunks > 1 && skipFlexiprep)) 0 else if (paired) 2 else 1)
mapping.functions.count(_.isInstanceOf[Seqstat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 4 else 2) * chunks)
mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)