diff --git a/external-example/.gitignore b/external-example/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..77146859b6e12b32e90cc6f6d388ebc878d548d6
--- /dev/null
+++ b/external-example/.gitignore
@@ -0,0 +1,14 @@
+# Project-related
+dependency-reduced-pom.xml
+git.properties
+
+# gedit
+*~
+# Vim
+*.swp
+# IntelliJ
+.idea/*
+*.iml
+target/
+public/target/
+protected/target/
diff --git a/external-example/README.md b/external-example/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..956c6ccf2746212b45f3650ef917147bdd9ed800
--- /dev/null
+++ b/external-example/README.md
@@ -0,0 +1 @@
+Test implementation of Magpie 2.0
\ No newline at end of file
diff --git a/external-example/pom.xml b/external-example/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..da0d2258fc90fe3cc9a49b76504be5388c683fa1
--- /dev/null
+++ b/external-example/pom.xml
@@ -0,0 +1,294 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <!--TODO: replace groupId -->
+ <groupId>org.example.group</groupId>
+
+ <!--TODO: replace artifactId -->
+ <artifactId>ExternalExample</artifactId>
+
+ <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
+ <version>0.1.0-SNAPSHOT</version>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <scoverage.plugin.version>1.0.4</scoverage.plugin.version>
+ <sting.shade.phase>package</sting.shade.phase>
+
+ <!--
+ TODO: replace app.main.class, this is the class that get executed when running the jar file
+ This can be any executable that have a main method. In Biopet any pipeline can be used as direct executable.
+ Value for direct pipeline: 'org.example.group.pipelines.SimplePipeline'
+ In the given example is an extension of the biopet executable. In this example there are multiple pipelines in 1 executable.
+
+ It's also possible to make your own main function and call the main function with it's argument of the pipeline from there.
+ -->
+ <app.main.class>org.example.group.ExecutableExample</app.main.class>
+ </properties>
+
+ <dependencies>
+ <!--
+ In here maven dependencies can be placed, when importing a biopet pipeline 'Biopet-Framework' is not required.
+ When only using the framework without pipeline you need to import BiopetFramework.
+ It's advised to not use different versions of the pipeline and the framework.
+ -->
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetCore</artifactId>
+
+ <!--TODO: replace version of pipeline to a fixed version -->
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Shiva</artifactId>
+
+ <!--TODO: replace version of pipeline to a fixed version -->
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
+ <testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
+ <testResources>
+ <testResource>
+ <directory>${basedir}/src/test/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
+ </testResource>
+ </testResources>
+ <resources>
+ <resource>
+ <directory>${basedir}/src/main/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
+ </resource>
+ </resources>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.4.1</version>
+ <configuration>
+ <!--suppress MavenModelInspection -->
+ <finalName>${project.artifactId}-${project.version}-${git.commit.id.abbrev}</finalName>
+ <transformers>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <manifestEntries>
+ <Main-Class>${app.main.class}</Main-Class>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+ </manifestEntries>
+ </transformer>
+ </transformers>
+ <filters>
+ </filters>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.18.1</version>
+ <configuration>
+ <forkCount>1C</forkCount>
+ <workingDirectory>${project.build.directory}</workingDirectory>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.10</version>
+ <executions>
+ <execution>
+ <id>copy-installed</id>
+ <phase>prepare-package</phase>
+ <goals>
+ <goal>list</goal>
+ </goals>
+ <configuration>
+ <outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>net.alchim31.maven</groupId>
+ <artifactId>scala-maven-plugin</artifactId>
+ <version>3.2.0</version>
+ <executions>
+ <execution>
+ <id>scala-compile</id>
+ <goals>
+ <goal>compile</goal>
+ <goal>testCompile</goal>
+ </goals>
+ <configuration>
+ <args>
+ <arg>-dependencyfile</arg>
+ <arg>${project.build.directory}/.scala_dependencies</arg>
+ <arg>-deprecation</arg>
+ <arg>-feature</arg>
+ </args>
+ </configuration>
+ </execution>
+ </executions>
+ <!-- ... (see other usage or goals for details) ... -->
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.5</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>test-jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <archive>
+ <manifest>
+ <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+ <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+ </manifest>
+ </archive>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
+ <configuration>
+ <showDeprecation>true</showDeprecation>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.scalariform</groupId>
+ <artifactId>scalariform-maven-plugin</artifactId>
+ <version>0.1.4</version>
+ <executions>
+ <execution>
+ <phase>process-sources</phase>
+ <goals>
+ <goal>format</goal>
+ </goals>
+ <configuration>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <alignParameters>true</alignParameters>
+ <alignSingleLineCaseStatements_maxArrowIndent>40
+ </alignSingleLineCaseStatements_maxArrowIndent>
+ <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
+ <compactStringConcatenation>false</compactStringConcatenation>
+ <compactControlReadability>false</compactControlReadability>
+ <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
+ <formatXml>true</formatXml>
+ <indentLocalDefs>false</indentLocalDefs>
+ <indentPackageBlocks>true</indentPackageBlocks>
+ <indentSpaces>2</indentSpaces>
+ <placeScaladocAsterisksBeneathSecondAsterisk>false
+ </placeScaladocAsterisksBeneathSecondAsterisk>
+ <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
+ <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <spaceBeforeColon>false</spaceBeforeColon>
+ <spaceInsideBrackets>false</spaceInsideBrackets>
+ <spaceInsideParentheses>false</spaceInsideParentheses>
+ <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>pl.project13.maven</groupId>
+ <artifactId>git-commit-id-plugin</artifactId>
+ <version>2.1.10</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>revision</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <prefix>git</prefix>
+ <dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
+ <verbose>false</verbose>
+ <!-- TODO: This directory need to be changed depening where your .git folder is relative from this pom.xml -->
+ <dotGitDirectory>${basedir}/../.git</dotGitDirectory>
+ <useNativeGit>true</useNativeGit>
+ <skipPoms>false</skipPoms>
+ <generateGitPropertiesFile>true</generateGitPropertiesFile>
+ <generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
+ <failOnNoGitDirectory>false</failOnNoGitDirectory>
+ <abbrevLength>8</abbrevLength>
+ <skip>false</skip>
+ <gitDescribe>
+ <skip>false</skip>
+ <always>false</always>
+ <abbrev>8</abbrev>
+ <dirty>-dirty</dirty>
+ <forceLongFormat>false</forceLongFormat>
+ </gitDescribe>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>com.mycila</groupId>
+ <artifactId>license-maven-plugin</artifactId>
+ <version>2.6</version>
+ <configuration>
+ <excludes>
+ <exclude>**/*git*</exclude>
+ <exclude>**/License*</exclude>
+ <exclude>**/*.bam</exclude>
+ <exclude>**/*.bai</exclude>
+ <exclude>**/*.gtf</exclude>
+ <exclude>**/*.fq</exclude>
+ <exclude>**/*.sam</exclude>
+ <exclude>**/*.bed</exclude>
+ <exclude>**/*.refFlat</exclude>
+ <exclude>**/*.R</exclude>
+ <exclude>**/*.rscript</exclude>
+ </excludes>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.scoverage</groupId>
+ <artifactId>scoverage-maven-plugin</artifactId>
+ <version>${scoverage.plugin.version}</version>
+ <configuration>
+ <scalaVersion>2.10.2</scalaVersion>
+ <!-- other parameters -->
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <reporting>
+ <plugins>
+ <plugin>
+ <groupId>org.scoverage</groupId>
+ <artifactId>scoverage-maven-plugin</artifactId>
+ <version>${scoverage.plugin.version}</version>
+ </plugin>
+ </plugins>
+ </reporting>
+</project>
\ No newline at end of file
diff --git a/external-example/src/main/scala/org/example/group/ExecutableExample.scala b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
new file mode 100644
index 0000000000000000000000000000000000000000..fe0aaa13d57d5380f8eb14bf984145992ce297e8
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
@@ -0,0 +1,19 @@
+package org.example.group
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+object ExecutableExample extends BiopetExecutable {
+
+ /** This list defines the pipeline that are usable from the executable */
+ def pipelines: List[MainCommand] = List(
+ org.example.group.pipelines.MultisamplePipeline,
+ org.example.group.pipelines.BiopetPipeline,
+ org.example.group.pipelines.SimplePipeline
+ )
+
+ /** This list defines the (biopet)tools that are usable from the executable */
+ def tools: List[MainCommand] = Nil
+}
diff --git a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..6099047a6e5153c15df565d3e70179006ef4ceac
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
@@ -0,0 +1,47 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 8/28/15.
+ */
+//TODO: Replace class Name
+class BiopetPipeline(val root: Configurable) extends QScript with SummaryQScript {
+ def this() = this(null)
+
+ /** Only required when using [[SummaryQScript]] */
+ def summaryFile = new File(outputDir, "magpie.summary.json")
+
+ /** Only required when using [[SummaryQScript]] */
+ def summaryFiles: Map[String, File] = Map()
+
+ /** Only required when using [[SummaryQScript]] */
+ def summarySettings = Map()
+
+ // This method can be used to initialize some classes where needed
+ def init(): Unit = {
+ }
+
+ // This method is the actual pipeline
+ def biopetScript: Unit = {
+
+ // Executing a biopet pipeline inside
+ val shiva = new Shiva(this)
+ shiva.init()
+ shiva.biopetScript()
+ addAll(shiva.functions)
+
+ /* Only required when using [[SummaryQScript]] */
+ addSummaryQScript(shiva)
+
+ // From here you can use the output files of shiva as input file of other jobs
+ }
+}
+
+//TODO: Replace object Name, must be the same as the class of the pipeline
+object BiopetPipeline extends PipelineCommand
diff --git a/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ee66d89663c22868958720615a83c5d72f85e8f7
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
@@ -0,0 +1,64 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+class MultisamplePipeline(val root: Configurable) extends QScript with MultiSampleQScript {
+ qscript =>
+ def this() = this(null)
+
+ def init: Unit = {
+ }
+
+ def biopetScript: Unit = {
+ addSamplesJobs() // This executes jobs for all samples
+ }
+
+ def addMultiSampleJobs: Unit = {
+ // this code will be executed after all code of all samples is executed
+ }
+
+ def summaryFile: File = new File(outputDir, "MultisamplePipeline.summary.json")
+
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summarySettings: Map[String, Any] = Map()
+
+ def makeSample(id: String) = new Sample(id)
+ class Sample(sampleId: String) extends AbstractSample(sampleId) {
+
+ def makeLibrary(id: String) = new Library(id)
+ class Library(libId: String) extends AbstractLibrary(libId) {
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summaryStats: Map[String, Any] = Map()
+
+ def addJobs: Unit = {
+ //TODO: add library specific jobs
+ }
+ }
+
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summaryStats: Map[String, Any] = Map()
+
+ def addJobs: Unit = {
+ addPerLibJobs() // This add jobs for each library
+ //TODO: add sample specific jobs
+ }
+ }
+
+}
+
+object MultisamplePipeline extends PipelineCommand
\ No newline at end of file
diff --git a/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f24b0f6152a03979d74c2f7337760cdc06c9e3be
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
@@ -0,0 +1,38 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Cat }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+//TODO: Replace class name, must be the same as the class of the pipeline
+class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript {
+ // A constructor without arguments is needed if this pipeline is a root pipeline
+ def this() = this(null)
+
+ @Input(required = true)
+ var inputFile: File = null
+
+ /** This method can be used to initialize some classes where needed */
+ def init(): Unit = {
+ }
+
+ /** This method is the actual pipeline */
+ def biopetScript: Unit = {
+ val cat = new Cat(this)
+ cat.input :+= inputFile
+ cat.output = new File(outputDir, "file.out")
+ add(cat)
+
+ val gzip = new Gzip(this)
+ gzip.input :+= cat.output
+ gzip.output = new File(outputDir, "file.out.gz")
+ add(gzip)
+ }
+}
+
+//TODO: Replace object name, must be the same as the class of the pipeline
+object SimplePipeline extends PipelineCommand
diff --git a/pom.xml b/pom.xml
index 9390bf9a13c0362d75f158b08d2e99d3ad8d181f..143a9095a763bbdcc323dc6e4299e534e5f0bc33 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,5 +16,6 @@
<modules>
<module>public</module>
<module>protected</module>
+ <module>external-example</module>
</modules>
</project>
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
index 203354565b98b05a36d8227859823ee721ae60ee..8b8ea7d5a97ca2095c981b1b11a3bae6496583a8 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
@@ -14,8 +14,8 @@ class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk
override val defaultThreads = 3
- override def beforeGraph() {
- super.beforeGraph()
+ override def freezeFieldValues() {
+ super.freezeFieldValues()
nt = Option(getThreads)
memoryLimit = Option(nt.getOrElse(1) * 2)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
index fbe2317e93d83c2fa6d3da58a9224dc6ba15a803..d51a28375b07aea9d3462f9d2b5f185fc2f4b629 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
@@ -20,7 +20,6 @@ object BaseRecalibrator {
val br = new BaseRecalibrator(root)
br.input_file :+= input
br.out = output
- br.beforeGraph()
br
}
}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index 1d8de140b277d349095ae459f700ed5437888b16..f0073f0116b99a92fcace99ec1979a907e29eb14 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
@@ -5,32 +5,39 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.core.{ CommandLineResources, Reference, BiopetJavaCommandLineFunction }
+import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
-trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
+trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference {
memoryLimit = Option(3)
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar")
+ reference_sequence = referenceFasta()
+
override def defaultCoreMemory = 4.0
override def faiRequired = true
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
+
+ Option(config("et").value) match {
+ case Some("NO_ET") => et = GATKRunReport.PhoneHomeOption.NO_ET
+ case Some("AWS") => et = GATKRunReport.PhoneHomeOption.AWS
+ case Some("STDOUT") => et = GATKRunReport.PhoneHomeOption.STDOUT
+ case Some(x) => throw new IllegalArgumentException(s"Unknown et option for gatk: $x")
+ case _ =>
+ }
+
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree")
- override def versionRegex = """(.*)""".r
- override def versionExitcode = List(0, 1)
- override def versionCommand = executable + " -jar " + jarFile + " -version"
-
- override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
+ //override def versionRegex = """(.*)""".r
+ //override def versionExitcode = List(0, 1)
+ //override def versionCommand = executable + " -jar " + jarFile + " -version"
- override def beforeGraph(): Unit = {
- super.beforeGraph()
- if (reference_sequence == null) reference_sequence = referenceFasta()
- }
+ //override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
index 30c7f890ac877194478119c9ee5187f283da6718..514879f9d2b96088a6e5b3e30eb969d44740934b 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
@@ -38,11 +38,11 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf = config("stand_emit_conf", default = 0)
}
- override def beforeGraph() {
- super.beforeGraph()
+ override def freezeFieldValues() {
+ super.freezeFieldValues()
if (bamOutput != null && nct.getOrElse(1) > 1) {
- threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
+ nCoresRequest = Some(1)
}
nct = Some(getThreads)
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
index a135b70c12e3f1deebb718b4ca788a9d0ebd5dce..70d988f4b057572bc1c110ad597c232d6093a2cc 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
@@ -28,8 +28,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
override val defaultThreads = 1
- override def beforeGraph() {
- super.beforeGraph()
+ override def freezeFieldValues() {
+ super.freezeFieldValues()
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
nct = Some(getThreads)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
index 9329c394d15bc0428a1c11077896a5026876be91..fdb6e7e27b08793f44fb94d82c5ceef0033d4ed5 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
@@ -10,9 +10,6 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
- override def beforeGraph() {
- super.beforeGraph()
- }
}
object VariantEval {
@@ -22,7 +19,6 @@ object VariantEval {
vareval.eval = Seq(sample)
vareval.comp = Seq(compareWith)
vareval.out = output
- vareval.beforeGraph()
vareval
}
@@ -36,7 +32,6 @@ object VariantEval {
vareval.ST = ST
vareval.noEV = true
vareval.EV = EV
- vareval.beforeGraph()
vareval
}
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index 9395daa1da479d97d5b5bd822379be5085b67c6c..66f0bfcc564503567782bcc1e35b0cc0899e6212 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -74,8 +74,6 @@ class ShivaTest extends TestNGSuite with Matchers {
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
- pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
// Gatk preprocess
@@ -93,6 +91,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object ShivaTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -136,8 +140,8 @@ object ShivaTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -145,8 +149,8 @@ object ShivaTest {
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
)
)
)))
@@ -154,12 +158,12 @@ object ShivaTest {
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("3_1_R1.fq"),
+ "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("3_2_R1.fq"),
+ "R2" -> inputTouch("3_2_R2.fq")
)
)
)))
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 2c60207a82fae9da823eb02d7a860b5dd8be1834..8e8a1eddf9e5d6b5aab36c4c6fea7d35ea2da82e 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -73,7 +73,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+ pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
val illegalArgumentException = pipeline.inputBams.isEmpty ||
(!raw && !bcftools &&
@@ -107,6 +107,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): File = {
+ val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+ Files.touch(file)
+ file
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
index 4e725bb0b1e2002a323cc22f38c86b53ca4f14af..9155e7dbacf4fd624694ac06a1ddf24c69071afe 100644
--- a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
+++ b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutableProtected extends BiopetExecutable {
- def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
+ def pipelines: List[MainCommand] = BiopetExecutablePublic.publicPipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.Shiva,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.Basty)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index 451350227e5620ae612212eb341e0acae49ad958..fb9e39611fd861f9158503581f17d4bd12e6cb30 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -35,6 +35,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
var bamFile: File = null
def init(): Unit = {
+ inputFiles :+= new InputFile(bamFile)
}
def biopetScript(): Unit = {
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
index 45f8da529dbab9bcd5c9a7dd6d93fd730b87715b..ba6692dd7af137c57e51d023438995f136d2e477 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
@@ -42,7 +42,7 @@
#end
#if (showPlot)
- #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }#
+ #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
<div class="panel-body">
<img src="insertsize.png" class="img-responsive" />
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
index 9905a23cfdcb9ac10ba96b1bb2ed43b3686604b8..e900774e0788d03fc5180444fbbb6bd875ad253e 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
@@ -36,7 +36,7 @@
#end
#if (showPlot)
- #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId) }#
+ #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
<div class="panel-body">
<img src="wgs.png" class="img-responsive" />
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 24b0a29b1a7ce265ea145f404203f614da550884..f6a6dc090defdb238f76b68f21189faf38fd207c 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -71,7 +71,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
/** executed before script */
- def init() {
+ def init(): Unit = {
+ inputFiles :+= new InputFile(inputBam)
}
/** Script to add jobs */
@@ -186,8 +187,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
object BamMetrics extends PipelineCommand {
/** Make default implementation of BamMetrics and runs script already */
- def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
+ def apply(root: Configurable,
+ bamFile: File, outputDir: File,
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): BamMetrics = {
val bamMetrics = new BamMetrics(root)
+ bamMetrics.sampleId = sampleId
+ bamMetrics.libId = libId
bamMetrics.inputBam = bamFile
bamMetrics.outputDir = outputDir
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index f4138e12ec607ecfdcc9538347c83fbe6c9d4d16..babc43f721b9a1bd4d03f6930a97e4cb454f4187 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -156,14 +156,15 @@ object BammetricsReport extends ReportBuilder {
prefix: String,
summary: Summary,
libraryLevel: Boolean = false,
- sampleId: Option[String] = None): Unit = {
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) {
tsvWriter.println((for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) yield s"$sample-$lib")
.mkString("library\t", "\t", ""))
} else {
@@ -198,7 +199,7 @@ object BammetricsReport extends ReportBuilder {
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) fill(sample, Some(lib))
} else if (sampleId.isDefined) fill(sampleId.get, None)
else summary.samples.foreach(fill(_, None))
@@ -208,7 +209,7 @@ object BammetricsReport extends ReportBuilder {
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
} else {
for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
@@ -243,14 +244,15 @@ object BammetricsReport extends ReportBuilder {
prefix: String,
summary: Summary,
libraryLevel: Boolean = false,
- sampleId: Option[String] = None): Unit = {
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) {
tsvWriter.println((for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) yield s"$sample-$lib")
.mkString("library\t", "\t", ""))
} else {
@@ -285,7 +287,7 @@ object BammetricsReport extends ReportBuilder {
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) fill(sample, Some(lib))
} else if (sampleId.isDefined) fill(sampleId.get, None)
else summary.samples.foreach(fill(_, None))
@@ -295,8 +297,10 @@ object BammetricsReport extends ReportBuilder {
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
- lib <- summary.libraries(sample)
- ) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+ ) {
+ tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+ }
} else {
for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
diff --git a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
index 7e97b4a78e1176b1603a7ae5aec10057c4bd0175..33304cb198807f46d3801ddfc9b05eaa7d555fe4 100644
--- a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
@@ -69,7 +69,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
val bammetrics: BamMetrics = initPipeline(map)
- bammetrics.inputBam = new File("input.bam")
+ bammetrics.inputBam = BamMetricsTest.bam
bammetrics.sampleId = Some("1")
bammetrics.libId = Some("1")
bammetrics.script()
@@ -98,6 +98,10 @@ class BamMetricsTest extends TestNGSuite with Matchers {
object BamMetricsTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val bam = new File(outputDir, "input" + File.separator + "bla.bam")
+ Files.touch(bam)
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
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 09528f1b674b6d48b49d022b3d79b82a3d31d9b9..d9085369f0316b6a0474fe02cd15ef07c683713a 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
@@ -89,6 +89,8 @@ trait BastyTrait extends MultiSampleQScript {
addAll(shiva.functions)
addSummaryQScript(shiva)
+ inputFiles :::= shiva.inputFiles
+
addSamplesJobs()
}
@@ -135,7 +137,6 @@ trait BastyTrait extends MultiSampleQScript {
val numBoot = config("boot_runs", default = 100, submodule = "raxml").asInt
val bootList = for (t <- 0 until numBoot) yield {
val raxmlBoot = new Raxml(this)
- raxmlBoot.threads = 1
raxmlBoot.input = variants
raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBoot.p = Some(seed)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 30c400bc52d8ab439089f238864858fa32ef6832..254e783cb9e31718a8b0759e7ce0d55c152d203d 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -15,25 +15,276 @@
*/
package nl.lumc.sasc.biopet.core
-/**
- * This class is for commandline programs where the executable is a non JVM based program
- */
-abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
+import java.io.{ PrintWriter, File, FileInputStream }
+import java.security.MessageDigest
+
+import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.runtime.ProcessSettings
+import org.ggf.drmaa.JobTemplate
+
+import scala.collection.mutable
+import scala.io.Source
+import scala.sys.process.{ Process, ProcessLogger }
+import scala.util.matching.Regex
+import scala.collection.JavaConversions._
+
+/** Biopet command line trait to auto check executable and cluster values */
+trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
+ analysisName = configName
+
+ @Input(doc = "deps", required = false)
+ var deps: List[File] = Nil
+
+ @Output
+ var outputFiles: List[File] = Nil
+
+ var executable: String = _
+
+ /** This is the default shell for drmaa jobs */
+ def defaultRemoteCommand = "bash"
+ private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)
+
+ private def changeScript(file: File): Unit = {
+ val lines = Source.fromFile(file).getLines().toList
+ val writer = new PrintWriter(file)
+ writer.println("set -eubf")
+ writer.println("set -o pipefail")
+ lines.foreach(writer.println(_))
+ writer.close()
+ }
+
+ // This overrides the default "sh" from queue. For Biopet the default is "bash"
+ updateJobRun = {
+ case jt: JobTemplate => {
+ changeScript(new File(jt.getArgs.head.toString))
+ jt.setRemoteCommand(remoteCommand)
+ }
+ case ps: ProcessSettings => {
+ changeScript(new File(ps.getCommand.tail.head))
+ ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
+ }
+ }
+
+ /**
+ * Can override this method. This is executed just before the job is ready to run.
+ * Can check on run time files from pipeline here
+ */
+ def beforeCmd() {}
+
+ /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
+ def beforeGraph() {}
+
+ override def freezeFieldValues() {
+ preProcessExecutable()
+ beforeGraph()
+ internalBeforeGraph()
+
+ super.freezeFieldValues()
+ }
+
+ /** Set default output file, threads and vmem for current job */
+ final def internalBeforeGraph(): Unit = {
+
+ pipesJobs.foreach(_.beforeGraph())
+ pipesJobs.foreach(_.internalBeforeGraph())
+
+ }
+
+ /** can override this value is executable may not be converted to CanonicalPath */
+ val executableToCanonicalPath = true
+
+ /**
+ * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
+ */
+ protected[core] def preProcessExecutable() {
+ if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+ if (executable != null) {
+ if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
+ try {
+ val oldExecutable = executable
+ val buffer = new StringBuffer()
+ val cmd = Seq("which", executable)
+ val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+ if (process.exitValue == 0) {
+ executable = buffer.toString
+ val file = new File(executable)
+ if (executableToCanonicalPath) executable = file.getCanonicalPath
+ else executable = file.getAbsolutePath
+ } else Logging.addError("executable: '" + executable + "' not found, please check config")
+ BiopetCommandLineFunction.executableCache += oldExecutable -> executable
+ BiopetCommandLineFunction.executableCache += executable -> executable
+ } catch {
+ case ioe: java.io.IOException =>
+ logger.warn(s"Could not use 'which' on '$executable', check on executable skipped: " + ioe)
+ }
+ } else executable = BiopetCommandLineFunction.executableCache(executable)
+
+ if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+ if (new File(executable).exists()) {
+ val is = new FileInputStream(executable)
+ val cnt = is.available
+ val bytes = Array.ofDim[Byte](cnt)
+ is.read(bytes)
+ is.close()
+ val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+ BiopetCommandLineFunction.executableMd5Cache += executable -> temp
+ } else BiopetCommandLineFunction.executableMd5Cache += executable -> "file_does_not_exist"
+ }
+ }
+ }
+ val md5 = BiopetCommandLineFunction.executableMd5Cache.get(executable)
+ addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
+ }
+
+ /** executes checkExecutable method and fill job report */
+ final protected def preCmdInternal() {
+ preProcessExecutable()
+ beforeCmd()
+
+ addJobReportBinding("cores", nCoresRequest match {
+ case Some(n) if n > 0 => n
+ case _ => 1
+ })
+ addJobReportBinding("version", getVersion)
+ }
+
+ /** Command to get version of executable */
+ protected[core] def versionCommand: String = null
+
+ /** Regex to get version from version command output */
+ protected[core] def versionRegex: Regex = null
+
+ /** Allowed exit codes for the version command */
+ protected[core] def versionExitcode = List(0)
+
+ /** Executes the version command */
+ private[core] def getVersionInternal: Option[String] = {
+ if (versionCommand == null || versionRegex == null) None
+ else getVersionInternal(versionCommand, versionRegex)
+ }
+
+ /** Executes the version command */
+ private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
+ if (versionCommand == null || versionRegex == null) return None
+ val exe = new File(versionCommand.trim.split(" ")(0))
+ if (!exe.exists()) return None
+ val stdout = new StringBuffer()
+ val stderr = new StringBuffer()
+ def outputLog = "Version command: \n" + versionCommand +
+ "\n output log: \n stdout: \n" + stdout.toString +
+ "\n stderr: \n" + stderr.toString
+ 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 None
+ }
+ for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
+ line match {
+ 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)
+ None
+ }
+
+ /** Get version from cache otherwise execute the version command */
+ def getVersion: Option[String] = {
+ if (!BiopetCommandLineFunction.executableCache.contains(executable))
+ preProcessExecutable()
+ if (!BiopetCommandLineFunction.versionCache.contains(versionCommand))
+ getVersionInternal match {
+ case Some(version) => BiopetCommandLineFunction.versionCache += versionCommand -> version
+ case _ =>
+ }
+ BiopetCommandLineFunction.versionCache.get(versionCommand)
+ }
+
+ private[core] var _inputAsStdin = false
+ def inputAsStdin = _inputAsStdin
+ private[core] var _outputAsStdout = false
+ def outputAsStsout = _outputAsStdout
+
+ /**
+ * This operator sends stdout to `that` and combine this into 1 command line function
+ * @param that Function that will read from stdin
+ * @return BiopetPipe function
+ */
+ def |(that: BiopetCommandLineFunction): BiopetCommandLineFunction = {
+ this._outputAsStdout = true
+ that._inputAsStdin = true
+ this.beforeGraph()
+ this.internalBeforeGraph()
+ that.beforeGraph()
+ that.internalBeforeGraph()
+ this match {
+ case p: BiopetPipe => {
+ p.commands.last._outputAsStdout = true
+ new BiopetPipe(p.commands ::: that :: Nil)
+ }
+ case _ => new BiopetPipe(List(this, that))
+ }
+ }
+
+ /**
+ * This operator can be used to give a program a file as stdin
+ * @param file File that will become stdin for this program
+ * @return It's own class
+ */
+ def :<:(file: File): BiopetCommandLineFunction = {
+ this._inputAsStdin = true
+ this.stdinFile = Some(file)
+ this
+ }
+
+ /**
+ * This operator can be used to give a program a file write it's atdout
+ * @param file File that will become stdout for this program
+ * @return It's own class
+ */
+ def >(file: File): BiopetCommandLineFunction = {
+ this._outputAsStdout = true
+ this.stdoutFile = Some(file)
+ this
+ }
+
+ @Output(required = false)
+ private[core] var stdoutFile: Option[File] = None
+
+ @Input(required = false)
+ private[core] var stdinFile: Option[File] = None
+
/**
* This function needs to be implemented to define the command that is executed
* @return Command to run
*/
- protected def cmdLine: String
+ protected[core] def cmdLine: String
/**
* implementing a final version of the commandLine from org.broadinstitute.gatk.queue.function.CommandLineFunction
* User needs to implement cmdLine instead
* @return Command to run
*/
- final def commandLine: String = {
+ override final def commandLine: String = {
preCmdInternal()
- val cmd = cmdLine
+ val cmd = cmdLine +
+ stdinFile.map(file => " < " + required(file.getAbsoluteFile)).getOrElse("") +
+ stdoutFile.map(file => " > " + required(file.getAbsoluteFile)).getOrElse("")
addJobReportBinding("command", cmd)
cmd
}
+
+ private[core] var pipesJobs: List[BiopetCommandLineFunction] = Nil
+ def addPipeJob(job: BiopetCommandLineFunction) {
+ pipesJobs :+= job
+ pipesJobs = pipesJobs.distinct
+ }
+}
+
+/** stores global caches */
+object BiopetCommandLineFunction {
+ private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
+ private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
+ private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
deleted file mode 100644
index 6084bb7b6a3b45f5ca184fe4c2634d8888846c77..0000000000000000000000000000000000000000
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ /dev/null
@@ -1,236 +0,0 @@
-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.core
-
-import java.io.{ File, FileInputStream }
-import java.security.MessageDigest
-
-import nl.lumc.sasc.biopet.utils.Logging
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.Input
-
-import scala.collection.mutable
-import scala.sys.process.{ Process, ProcessLogger }
-import scala.util.matching.Regex
-
-/** Biopet command line trait to auto check executable and cluster values */
-trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
- analysisName = configName
-
- @Input(doc = "deps", required = false)
- var deps: List[File] = Nil
-
- var threads = 0
- def defaultThreads = 1
-
- var vmem: Option[String] = config("vmem")
- protected def defaultCoreMemory: Double = 1.0
- protected def defaultVmemFactor: Double = 1.4
- var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
-
- var residentFactor: Double = config("resident_factor", default = 1.2)
-
- private var coreMemory: Double = _
-
- var executable: String = _
-
- /**
- * Can override this method. This is executed just before the job is ready to run.
- * Can check on run time files from pipeline here
- */
- protected[core] def beforeCmd() {}
-
- /** 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 */
- override def freezeFieldValues() {
- preProcessExecutable()
- beforeGraph()
- if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
-
- if (threads == 0) threads = getThreads(defaultThreads)
- if (threads > 1) nCoresRequest = Option(threads)
-
- coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
-
- if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
- else memoryLimit = Some(coreMemory * threads)
-
- if (config.contains("resident_limit")) residentLimit = config("resident_limit")
- else residentLimit = Some((coreMemory + (0.5 * retry)) * residentFactor)
-
- if (!config.contains("vmem")) vmem = Some((coreMemory * (vmemFactor + (0.5 * retry))) + "G")
- if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
- jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
-
- super.freezeFieldValues()
- }
-
- var retry = 0
-
- override def setupRetry(): Unit = {
- super.setupRetry()
- if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
- logger.info("Auto raise memory on retry")
- retry += 1
- this.freeze()
- }
-
- /** can override this value is executable may not be converted to CanonicalPath */
- val executableToCanonicalPath = true
-
- /**
- * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
- */
- protected[core] def preProcessExecutable() {
- if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
- try if (executable != null) {
- if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
- val oldExecutable = executable
- val buffer = new StringBuffer()
- val cmd = Seq("which", executable)
- val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
- if (process.exitValue == 0) {
- executable = buffer.toString
- val file = new File(executable)
- if (executableToCanonicalPath) executable = file.getCanonicalPath
- else executable = file.getAbsolutePath
- } else {
- Logging.addError("executable: '" + executable + "' not found, please check config")
- }
- BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
- BiopetCommandLineFunctionTrait.executableCache += executable -> executable
- } else {
- executable = BiopetCommandLineFunctionTrait.executableCache(executable)
- }
-
- if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
- val is = new FileInputStream(executable)
- val cnt = is.available
- val bytes = Array.ofDim[Byte](cnt)
- is.read(bytes)
- is.close()
- val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
- BiopetCommandLineFunctionTrait.executableMd5Cache += executable -> temp
- }
- } catch {
- case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
- }
- }
- val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
- addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
- }
-
- /** executes checkExecutable method and fill job report */
- final protected def preCmdInternal() {
- preProcessExecutable()
- beforeCmd()
-
- addJobReportBinding("cores", nCoresRequest match {
- case Some(n) if n > 0 => n
- case _ => 1
- })
- addJobReportBinding("version", getVersion)
- }
-
- /** Command to get version of executable */
- protected def versionCommand: String = null
-
- /** Regex to get version from version command output */
- protected def versionRegex: Regex = null
-
- /** Allowed exit codes for the version command */
- protected def versionExitcode = List(0)
-
- /** Executes the version command */
- private[core] def getVersionInternal: Option[String] = {
- if (versionCommand == null || versionRegex == null) None
- else getVersionInternal(versionCommand, versionRegex)
- }
-
- /** Executes the version command */
- private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
- if (versionCommand == null || versionRegex == null) return None
- val exe = new File(versionCommand.trim.split(" ")(0))
- if (!exe.exists()) return None
- val stdout = new StringBuffer()
- val stderr = new StringBuffer()
- def outputLog = "Version command: \n" + versionCommand +
- "\n output log: \n stdout: \n" + stdout.toString +
- "\n stderr: \n" + stderr.toString
- 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 None
- }
- for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
- line match {
- 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)
- None
- }
-
- /** Get version from cache otherwise execute the version command */
- def getVersion: Option[String] = {
- if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
- preProcessExecutable()
- if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
- getVersionInternal match {
- case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
- case _ =>
- }
- BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
- }
-
- def getThreads: Int = getThreads(defaultThreads)
-
- /**
- * Get threads from config
- * @param default default when not found in config
- * @return number of threads
- */
- def getThreads(default: Int): Int = {
- val maxThreads: Int = config("maxthreads", default = 24)
- val threads: Int = config("threads", default = default)
- if (maxThreads > threads) threads
- else maxThreads
- }
-
- /**
- * Get threads from config
- * @param default default when not found in config
- * @param module Module when this is difrent from default
- * @return number of threads
- */
- def getThreads(default: Int, module: String): Int = {
- val maxThreads: Int = config("maxthreads", default = 24, submodule = module)
- val threads: Int = config("threads", default = default, submodule = module)
- if (maxThreads > threads) threads
- else maxThreads
- }
-}
-
-/** stores global caches */
-object BiopetCommandLineFunctionTrait {
- private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
- private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
- private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
-}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ee06edb0a666a543c108c891092d5ac8ca7e23a6
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
@@ -0,0 +1,150 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by pjvan_thof on 9/29/15.
+ */
+class BiopetFifoPipe(val root: Configurable,
+ protected var commands: List[BiopetCommandLineFunction]) extends BiopetCommandLineFunction {
+
+ def fifos: List[File] = {
+ val outputs: Map[BiopetCommandLineFunction, Seq[File]] = try {
+ commands.map(x => x -> x.outputs).toMap
+ } catch {
+ case e: NullPointerException => Map()
+ }
+
+ val inputs: Map[BiopetCommandLineFunction, Seq[File]] = try {
+ commands.map(x => x -> x.inputs).toMap
+ } catch {
+ case e: NullPointerException => Map()
+ }
+
+ for (
+ cmdOutput <- commands;
+ cmdInput <- commands if cmdOutput != cmdInput && outputs.contains(cmdOutput);
+ outputFile <- outputs(cmdOutput) if inputs.contains(cmdInput);
+ inputFile <- inputs(cmdInput) if outputFile == inputFile
+ ) yield outputFile
+ }
+
+ override def beforeGraph(): Unit = {
+ val outputs: Map[BiopetCommandLineFunction, Seq[File]] = try {
+ commands.map(x => x -> x.outputs).toMap
+ } catch {
+ case e: NullPointerException => Map()
+ }
+
+ val inputs: Map[BiopetCommandLineFunction, Seq[File]] = try {
+ commands.map(x => x -> x.inputs).toMap
+ } catch {
+ case e: NullPointerException => Map()
+ }
+
+ val fifoFiles = fifos
+
+ outputFiles :::= outputs.values.toList.flatten.filter(!fifoFiles.contains(_))
+ outputFiles = outputFiles.distinct
+
+ deps :::= inputs.values.toList.flatten.filter(!fifoFiles.contains(_))
+ deps = deps.distinct
+ }
+
+ override def beforeCmd(): Unit = {
+ commands.foreach { cmd =>
+ cmd.beforeGraph()
+ cmd.internalBeforeGraph()
+ cmd.beforeCmd()
+ }
+ }
+
+ def cmdLine = {
+ val fifosFiles = this.fifos
+ fifosFiles.filter(_.exists()).map(required("rm", _)).mkString("\n\n", " \n", " \n\n") +
+ fifosFiles.map(required("mkfifo", _)).mkString("\n\n", "\n", "\n\n") +
+ commands.map(_.commandLine).mkString("\n\n", " & \n", " & \n\n") +
+ BiopetFifoPipe.waitScript +
+ fifosFiles.map(required("rm", _)).mkString("\n\n", " \n", " \n\n") +
+ BiopetFifoPipe.endScript
+ }
+
+ override def setResources(): Unit = {
+ combineResources(commands)
+ }
+
+ override def setupRetry(): Unit = {
+ super.setupRetry()
+ commands.foreach(_.setupRetry())
+ combineResources(commands)
+ }
+
+ override def freezeFieldValues(): Unit = {
+ super.freezeFieldValues()
+ commands.foreach(_.qSettings = qSettings)
+ }
+}
+
+object BiopetFifoPipe {
+ val waitScript =
+ """
+ |
+ |allJobs=`jobs -p`
+ |jobs=$allJobs
+ |
+ |echo [`date`] pids: $jobs
+ |
+ |FAIL="0"
+ |
+ |while echo $jobs | grep -e "\w" > /dev/null
+ |do
+ | for job in $jobs
+ | do
+ | if ps | grep "$job " | grep -v grep > /dev/null
+ | then
+ | echo [`date`] $job still running > /dev/null
+ | else
+ | jobs=`echo $jobs | sed "s/${job}//"`
+ | wait $job || FAIL=$?
+ | if echo $FAIL | grep -ve "^0$" > /dev/null
+ | then
+ | echo [`date`] $job fails with exitcode: $FAIL
+ | break
+ | fi
+ | echo [`date`] $job done
+ | fi
+ | done
+ | if echo $FAIL | grep -ve "^0$" > /dev/null
+ | then
+ | break
+ | fi
+ | sleep 1
+ |done
+ |
+ |if echo $FAIL | grep -ve "^0$" > /dev/null
+ |then
+ | echo [`date`] kill other pids: $jobs
+ | kill $jobs
+ |fi
+ |
+ |echo [`date`] Done
+ |
+ |
+ """.stripMargin
+
+ val endScript =
+ """
+ |
+ |if [ "$FAIL" == "0" ];
+ |then
+ |echo [`date`] "BiopetFifoPipe Done"
+ |else
+ |echo [`date`] BiopetFifoPipe "FAIL! ($FAIL)"
+ |exit $FAIL
+ |fi
+ |
+ |
+ """.stripMargin
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index d51442e3a25fbd030c16e3e126802e58cc6c2064..3f75cb92128b26bfb2681a2a25cfb5436c9ac5f6 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -18,38 +18,49 @@ package nl.lumc.sasc.biopet.core
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
/** Biopet commandline class for java based programs */
-trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
+trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunction {
executable = config("java", default = "java", submodule = "java", freeVar = false)
javaGCThreads = config("java_gc_threads")
javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
javaGCTimeLimit = config("java_gc_timelimit")
- override protected def defaultVmemFactor: Double = 2.0
+ override def defaultVmemFactor: Double = 2.0
/** Constructs java opts, this adds scala threads */
override def javaOpts = super.javaOpts +
- optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
+ optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false)
+
+ override def beforeGraph(): Unit = {
+ setResources()
+ if (javaMemoryLimit.isEmpty && memoryLimit.isDefined)
+ javaMemoryLimit = memoryLimit
+
+ if (javaMainClass != null && javaClasspath.isEmpty)
+ javaClasspath = JavaCommandLineFunction.currentClasspath
+
+ //threads = getThreads(defaultThreads)
+ }
/** Creates command to execute extension */
- override def commandLine: String = {
+ def cmdLine: String = {
preCmdInternal()
- val cmd = super.commandLine
- val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
- cmd
+ required(executable) +
+ javaOpts +
+ javaExecutable
}
def javaVersionCommand: String = executable + " -version"
def getJavaVersion: Option[String] = {
- if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
+ if (!BiopetCommandLineFunction.executableCache.contains(executable))
preProcessExecutable()
- if (!BiopetCommandLineFunctionTrait.versionCache.contains(javaVersionCommand))
+ if (!BiopetCommandLineFunction.versionCache.contains(javaVersionCommand))
getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
- case Some(version) => BiopetCommandLineFunctionTrait.versionCache += javaVersionCommand -> version
+ case Some(version) => BiopetCommandLineFunction.versionCache += javaVersionCommand -> version
case _ =>
}
- BiopetCommandLineFunctionTrait.versionCache.get(javaVersionCommand)
+ BiopetCommandLineFunction.versionCache.get(javaVersionCommand)
}
override def setupRetry(): Unit = {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
new file mode 100644
index 0000000000000000000000000000000000000000..8b5e9fbaefe84175828c9a3f844c2120bb9ba259
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
@@ -0,0 +1,74 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * This class can pipe multiple BiopetCommandFunctions to 1 job
+ *
+ * Created by pjvanthof on 08/09/15.
+ */
+class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCommandLineFunction {
+
+ @Input
+ lazy val input: List[File] = try {
+ commands.flatMap(_.inputs)
+ } catch {
+ case e: Exception => Nil
+ }
+
+ @Output
+ lazy val output: List[File] = try {
+ commands.flatMap(_.outputs)
+ } catch {
+ case e: Exception => Nil
+ }
+
+ pipesJobs :::= commands
+
+ override def beforeGraph() {
+ super.beforeGraph()
+
+ stdoutFile = stdoutFile.map(_.getAbsoluteFile)
+ stdinFile = stdinFile.map(_.getAbsoluteFile)
+
+ if (stdoutFile.isDefined || _outputAsStdout) {
+ commands.last.stdoutFile = None
+ commands.last._outputAsStdout = true
+ }
+
+ if (commands.head.stdinFile.isDefined) commands.head._inputAsStdin = true
+
+ val inputOutput = input.filter(x => output.contains(x))
+ require(inputOutput.isEmpty, "File found as input and output in the same job, files: " + inputOutput.mkString(", "))
+ }
+
+ override def setResources(): Unit = {
+ combineResources(pipesJobs)
+ }
+
+ override def setupRetry(): Unit = {
+ super.setupRetry()
+ commands.foreach(_.setupRetry())
+ combineResources(commands)
+ }
+
+ override def defaultCoreMemory = 0.0
+ override def defaultThreads = 0
+
+ val root: Configurable = commands.head.root
+ override def configName = commands.map(_.configName).mkString("-")
+ def cmdLine: String = {
+ "(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) {
+ " < " + required(commands.head.stdinFile.map(_.getAbsoluteFile))
+ } else "") + " | " + commands.tail.map(_.cmdLine).mkString(" | ") +
+ (if (commands.last.stdoutFile.isDefined) " > " + required(commands.last.stdoutFile.map(_.getAbsoluteFile)) else "") + ")"
+ }
+
+ override def freezeFieldValues(): Unit = {
+ super.freezeFieldValues()
+ commands.foreach(_.qSettings = qSettings)
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index f35c07a0a4497fa4a36e0b34a1b640cf8f03364c..1109f30da9fcb53cd622935b8451d6ab551d0205 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -48,6 +48,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
var outputFiles: Map[String, File] = Map()
+ type InputFile = BiopetQScript.InputFile
+
+ var inputFiles: List[InputFile] = Nil
+
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
var qSettings: QSettings
@@ -75,9 +79,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ =>
}
for (function <- functions) function match {
- case f: BiopetCommandLineFunctionTrait =>
+ case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
f.beforeGraph()
+ f.internalBeforeGraph()
f.commandLine
case _ =>
}
@@ -86,7 +91,16 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
- reportClass.foreach(add(_))
+ inputFiles.foreach { i =>
+ if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
+ else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
+ }
+
+ this match {
+ case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+ logger.info("Write report is skipped because sample flag is used")
+ case _ => reportClass.foreach(add(_))
+ }
Logging.checkErrors()
}
@@ -103,3 +117,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
add(function)
}
}
+
+object BiopetQScript {
+ protected case class InputFile(file: File, md5: Option[String] = None)
+}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
new file mode 100644
index 0000000000000000000000000000000000000000..300cd4cdb0d240f19c709ac53e35b180e8675504
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
@@ -0,0 +1,98 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+
+/**
+ * Created by pjvanthof on 01/10/15.
+ */
+trait CommandLineResources extends CommandLineFunction with Configurable {
+
+ def defaultThreads = 1
+ final def threads = nCoresRequest match {
+ case Some(i) => i
+ case _ => {
+ val t = getThreads
+ nCoresRequest = Some(t)
+ t
+ }
+ }
+
+ var vmem: Option[String] = config("vmem")
+ def defaultCoreMemory: Double = 1.0
+ def defaultVmemFactor: Double = 1.4
+ var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
+
+ var residentFactor: Double = config("resident_factor", default = 1.2)
+
+ private var _coreMemory: Double = 2.0
+ def coreMemeory = _coreMemory
+
+ var retry = 0
+
+ override def freezeFieldValues(): Unit = {
+ setResources()
+ if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
+ super.freezeFieldValues()
+ }
+
+ def getThreads: Int = getThreads(defaultThreads)
+
+ /**
+ * Get threads from config
+ * @param default default when not found in config
+ * @return number of threads
+ */
+ private def getThreads(default: Int): Int = {
+ val maxThreads: Int = config("maxthreads", default = 24)
+ val threads: Int = config("threads", default = default)
+ if (maxThreads > threads) threads
+ else maxThreads
+ }
+
+ def setResources(): Unit = {
+ val firstOutput = try {
+ this.firstOutput
+ } catch {
+ case e: NullPointerException => null
+ }
+
+ if (jobOutputFile == null && firstOutput != null)
+ jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
+
+ nCoresRequest = Option(threads)
+
+ _coreMemory = config("core_memory", default = defaultCoreMemory).asDouble +
+ (0.5 * retry)
+
+ if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
+ else memoryLimit = Some(_coreMemory * threads)
+
+ if (config.contains("resident_limit")) residentLimit = config("resident_limit")
+ else residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
+
+ if (!config.contains("vmem")) vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")
+ jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
+ }
+
+ override def setupRetry(): Unit = {
+ super.setupRetry()
+ if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
+ logger.info("Auto raise memory on retry")
+ retry += 1
+ this.freeze()
+ }
+
+ protected def combineResources(commands: List[CommandLineResources]): Unit = {
+ commands.foreach(_.setResources())
+ nCoresRequest = Some(commands.map(_.threads).sum)
+
+ _coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
+ memoryLimit = Some(_coreMemory * threads)
+ residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
+ vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")
+ }
+
+}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index d8756c7b91cd27b330b4697aab0d94c9f436c98a..17631709f12db8a3e3b25253afc49fadd3820e32 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -26,7 +26,7 @@ trait MultiSampleQScript extends SummaryQScript {
qscript =>
@Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
- private val onlySamples: List[String] = Nil
+ private[core] val onlySamples: List[String] = Nil
require(globalConfig.map.contains("samples"), "No Samples found in config")
@@ -131,7 +131,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
- if (onlySamples.isEmpty) {
+ if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
addMultiSampleJobs()
} else onlySamples.foreach(sampleId => samples.get(sampleId) match {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index 7a7013fd6dd8eecec23b33801894ef660fc22660..be479a8fa972fe896fb8d45cd74708944ba4ba64 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -74,8 +74,8 @@ trait Reference extends Configurable {
val fai = new File(file.getAbsolutePath + ".fai")
this match {
- case c: BiopetCommandLineFunctionTrait => c.deps :::= dict :: fai :: Nil
- case _ =>
+ case c: BiopetCommandLineFunction => c.deps :::= dict :: fai :: Nil
+ case _ =>
}
file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
index dcb50896014e5c6b96fc9940a74a0dacabc94bd8..81220f9cb9d56703dfd7bebcddc0c14fa9966e0d 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
@@ -10,6 +10,11 @@ trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
override def getVersion = Some("Biopet " + FullVersion)
+ override def beforeGraph(): Unit = {
+ javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
+ super.beforeGraph()
+ }
+
override def freezeFieldValues(): Unit = {
javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
super.freezeFieldValues()
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
new file mode 100644
index 0000000000000000000000000000000000000000..0ae2587f7928bb8d8cfe3e157f79fec7afff031a
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
@@ -0,0 +1,40 @@
+package nl.lumc.sasc.biopet.core.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
+
+/**
+ * This class checks md5sums and give an exit code 1 when md5sum is not the same
+ *
+ * Created by pjvanthof on 16/08/15.
+ */
+class CheckChecksum extends InProcessFunction {
+ @Input(required = true)
+ var inputFile: File = _
+
+ @Input(required = true)
+ var checksumFile: File = _
+
+ @Argument(required = true)
+ var checksum: String = _
+
+ override def freezeFieldValues(): Unit = {
+ super.freezeFieldValues()
+ jobOutputFile = new File(checksumFile.getParentFile, checksumFile.getName + ".check.out")
+ }
+
+ /** Exits whenever the input md5sum is not the same as the output md5sum */
+ def run: Unit = {
+ val outputChecksum = WriteSummary.parseChecksum(checksumFile).toLowerCase
+
+ if (outputChecksum != checksum.toLowerCase) {
+ logger.error(s"Input file: '$inputFile' md5sum is not as expected, aborting pipeline")
+
+ // 130 Simulates a ctr-C
+ Runtime.getRuntime.halt(130)
+ }
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index 6c1bc388153f37d746cbf8a173a5ecc85c7201d5..ae7c08e8eb1d20e68d238a5fe4bb3a1f48306626 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -54,8 +54,8 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
}
/** Command to generate the report */
- override def commandLine: String = {
- super.commandLine +
+ override def cmdLine: String = {
+ super.cmdLine +
required("--summary", summaryFile) +
required("--outputDir", outputDir) +
args.map(x => required("-a", x._1 + "=" + x._2)).mkString
@@ -231,6 +231,7 @@ object ReportBuilder {
case Some(template) => template
case _ =>
val tempFile = File.createTempFile("ssp-template", new File(location).getName)
+ tempFile.deleteOnExit()
IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
templateCache += location -> tempFile
tempFile
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 52c77fe8a63a090f2c4bb776da39647f9a35379e..ab2f64546a7f79e8432ec1ac7ff0ab19427cccfc 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.extensions.Md5sum
+import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
import scala.collection.mutable
@@ -27,7 +27,7 @@ import scala.collection.mutable
*
* Created by pjvan_thof on 2/14/15.
*/
-trait SummaryQScript extends BiopetQScript {
+trait SummaryQScript extends BiopetQScript { qscript =>
/** Key is sample/library, None is sample or library is not applicable */
private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
@@ -116,10 +116,24 @@ trait SummaryQScript extends BiopetQScript {
//TODO: add more checksums types
}
+ for (inputFile <- inputFiles) {
+ inputFile.md5 match {
+ case Some(checksum) => {
+ val checkMd5 = new CheckChecksum
+ checkMd5.inputFile = inputFile.file
+ require(SummaryQScript.md5sumCache.contains(inputFile.file), "Md5 job is not executed, checksum file can't be found")
+ checkMd5.checksumFile = SummaryQScript.md5sumCache(inputFile.file)
+ checkMd5.checksum = checksum
+ add(checkMd5)
+ }
+ case _ =>
+ }
+ }
+
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList) {
summarizable match {
- case f: BiopetCommandLineFunctionTrait => f.beforeGraph()
- case _ =>
+ case f: BiopetCommandLineFunction => f.beforeGraph()
+ case _ =>
}
}
@@ -135,7 +149,11 @@ trait SummaryQScript extends BiopetQScript {
for ((_, file) <- this.summaryFiles)
addChecksum(file)
- add(writeSummary)
+ this match {
+ case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+ logger.info("Write summary is skipped because sample flag is used")
+ case _ => add(writeSummary)
+ }
}
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 3db4607d6288f84b204033ee3db186ee76771935..6e7f8248c0693ed0df4c3a372b8885e1908187a7 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, BiopetJavaCommandLineFunction, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetJavaCommandLineFunction, SampleLibraryTag }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
@@ -71,16 +71,16 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val files = parseFiles(qscript.summaryFiles)
val settings = qscript.summarySettings
val executables: Map[String, Any] = {
- (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
+ (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunction]) yield {
f match {
case f: BiopetJavaCommandLineFunction =>
f.configName -> Map("version" -> f.getVersion.getOrElse(None),
- "java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
+ "java_md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
"java_version" -> f.getJavaVersion,
"jar_path" -> f.jarFile)
case f: BiopetCommandLineFunction =>
f.configName -> Map("version" -> f.getVersion.getOrElse(None),
- "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
+ "md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
"path" -> f.executable)
case _ => throw new IllegalStateException("This should not be possible")
}
@@ -153,10 +153,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
def parseFile(file: File): Map[String, Any] = {
val map: mutable.Map[String, Any] = mutable.Map()
map += "path" -> file.getAbsolutePath
- if (md5sum) map += "md5" -> parseChecksum(SummaryQScript.md5sumCache(file))
+ if (md5sum) map += "md5" -> WriteSummary.parseChecksum(SummaryQScript.md5sumCache(file))
map.toMap
}
-
+}
+object WriteSummary {
/** Retrive checksum from file */
def parseChecksum(checksumFile: File): String = {
Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..bac6932ddecd94dcbeb6ff6648edd5461ddced13
--- /dev/null
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
@@ -0,0 +1,45 @@
+package nl.lumc.sasc.biopet.core
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 09/09/15.
+ */
+class BiopetPipeTest extends TestNGSuite with Matchers {
+ class Pipe1 extends BiopetCommandLineFunction {
+ val root = null
+ def cmdLine = "pipe1" +
+ (if (!inputAsStdin) " input1 " else "") +
+ (if (!outputAsStsout) " output1 " + "")
+ }
+
+ class Pipe2 extends BiopetCommandLineFunction {
+ val root = null
+ def cmdLine = "pipe2" +
+ (if (!inputAsStdin) " input2 " else "") +
+ (if (!outputAsStsout) " output2 " + "")
+ }
+
+ @Test def testPipeCommands: Unit = {
+ val pipe1 = new Pipe1
+ val pipe2 = new Pipe2
+ pipe1.commandLine.contains("pipe1") shouldBe true
+ pipe1.commandLine.contains("input1") shouldBe true
+ pipe1.commandLine.contains("output1") shouldBe true
+ pipe2.commandLine.contains("pipe2") shouldBe true
+ pipe2.commandLine.contains("input2") shouldBe true
+ pipe2.commandLine.contains("output2") shouldBe true
+ }
+
+ @Test def testPipe: Unit = {
+ val pipe = new Pipe1 | new Pipe2
+ pipe.commandLine.contains("pipe1") shouldBe true
+ pipe.commandLine.contains("input1") shouldBe true
+ pipe.commandLine.contains("output1") shouldBe false
+ pipe.commandLine.contains("pipe2") shouldBe true
+ pipe.commandLine.contains("input2") shouldBe false
+ pipe.commandLine.contains("output2") shouldBe true
+ }
+}
diff --git a/public/biopet-extentsions/pom.xml b/public/biopet-extensions/pom.xml
similarity index 100%
rename from public/biopet-extentsions/pom.xml
rename to public/biopet-extensions/pom.xml
diff --git a/public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
similarity index 100%
rename from public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
rename to public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
similarity index 89%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
index 74901be9ca04722b54877032e0654d14d057ceb4..695b5ca3ae5e6943a4da481714a6bf1c7aa7c855 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
@@ -34,13 +34,17 @@ class Cat(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "cat")
/** return commandline to execute */
- def cmdLine = required(executable) + repeat(input) + " > " + required(output)
+ def cmdLine = required(executable) +
+ (if (inputAsStdin) "" else repeat(input)) +
+ (if (outputAsStsout) "" else " > " + required(output))
}
/**
* Object for constructors for cat
*/
object Cat {
+ def apply(root: Configurable): Cat = new Cat(root)
+
/**
* Basis constructor
* @param root root object for config
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
similarity index 97%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index f6278426ee4f76c8b4cca1cc1a40863ce22b24eb..43dd6826912c4390f0ac30148081536ac3ac7d05 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -33,7 +33,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
@Input(doc = "Input fastq file")
var fastq_input: File = _
- @Output(doc = "Output fastq file")
+ @Output
var fastq_output: File = _
@Output(doc = "Output statistics file")
@@ -63,8 +63,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
optional("-M", opt_maximum_length) +
// input / output
required(fastq_input) +
- required("--output", fastq_output) +
- " > " + required(stats_output)
+ (if (outputAsStsout) "" else required("--output", fastq_output) +
+ " > " + required(stats_output))
/** Output summary stats */
def summaryStats: Map[String, Any] = {
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
similarity index 84%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
index cdd44e6b2ba95ceff528ad4c136ade3c693cb03f..98bd00339c83e2a955372da3344c7a1f5debb257 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
@@ -28,15 +28,19 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Unzipped file", required = true)
var output: File = _
- executable = config("exe", default = "gzip")
+ executable = config("exe", default = "gzip", freeVar = false)
override def versionRegex = """gzip (.*)""".r
override def versionCommand = executable + " --version"
- def cmdLine = required(executable) + " -c " + repeat(input) + " > " + required(output)
+ def cmdLine = required(executable) + " -c " +
+ (if (inputAsStdin) "" else repeat(input)) +
+ (if (outputAsStsout) "" else " > " + required(output))
}
object Gzip {
+ def apply(root: Configurable): Gzip = new Gzip(root)
+
def apply(root: Configurable, input: List[File], output: File): Gzip = {
val gzip = new Gzip(root)
gzip.input = input
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index ae017f08881677cb60620f0f860c1dea2765ccee..f2f6eb21b9eaa2dc9956429906723f72f4400ee4 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -74,7 +74,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
/** Sets correct output files to job */
override def beforeGraph() {
require(w != null)
- if (threads == 0) threads = getThreads
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
super.beforeGraph()
out :::= List(Some(getInfoFile), getBestTreeFile, getBootstrapFile, getBipartitionsFile).flatten
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
similarity index 97%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index 53539ac9f9ae9ca46e3a7543e5375e690e916e6a..5334ab9cfe64a98f2d4c81745404c11006884044 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -34,9 +34,6 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Fasta file", shortName = "FQ")
var fastafile: File = _
- @Output(doc = "Output", shortName = "out")
- var outputFiles: List[File] = Nil
-
@Argument(required = true)
var outputDirectory: File = null
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
similarity index 93%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 938d36e432f9162942980f0da99be084bf455fa8..fe88be1adc2bda814157a0578ff9e4bfa622fb0a 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -36,7 +36,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
@Input(doc = "R2 input", required = false)
var input_R2: File = _
- @Output(doc = "R1 output")
+ @Output(doc = "R1 output", required = false)
var output_R1: File = _
@Output(doc = "R2 output", required = false)
@@ -48,8 +48,6 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
@Output(doc = "stats output")
var output_stats: File = _
- var fastqc: Fastqc = _
-
executable = config("exe", default = "sickle", freeVar = false)
var qualityType: Option[String] = config("qualitytype")
var qualityThreshold: Option[Int] = config("qualityThreshold")
@@ -76,15 +74,15 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
required("-s", output_singles)
} else cmd += required("se")
cmd +
- required("-f", input_R1) +
+ (if (inputAsStdin) required("-f", new File("/dev/stdin")) else required("-f", input_R1)) +
required("-t", qualityType) +
- required("-o", output_R1) +
+ (if (outputAsStsout) required("-o", new File("/dev/stdout")) else required("-o", output_R1)) +
optional("-q", qualityThreshold) +
optional("-l", lengthThreshold) +
conditional(noFiveprime, "-x") +
conditional(discardN, "-n") +
- conditional(quiet, "--quiet") +
- " > " + required(output_stats)
+ conditional(quiet || outputAsStsout, "--quiet") +
+ (if (outputAsStsout) "" else " > " + required(output_stats))
}
/** returns stats map for summary */
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
similarity index 73%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
index 974f5e9140be562da77bd4f167888b6945d9a70b..5c7ebd0ca6382584bc45b455527e50bdede1a673 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
@@ -23,10 +23,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for zcat */
class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
- @Input(doc = "Zipped file")
- var input: File = _
+ @Input(doc = "Zipped file", required = true)
+ var input: List[File] = _
- @Output(doc = "Unzipped file")
+ @Output(doc = "Unzipped file", required = true)
var output: File = _
executable = config("exe", default = "zcat")
@@ -35,12 +35,24 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
/** Returns command to execute */
- def cmdLine = required(executable) + required(input) + " > " + required(output)
+ def cmdLine = required(executable) +
+ (if (inputAsStdin) "" else required(input)) +
+ (if (outputAsStsout) "" else " > " + required(output))
}
object Zcat {
/** Returns a default zcat */
+ def apply(root: Configurable): Zcat = new Zcat(root)
+
+ /** Returns Zcat with input and output files */
def apply(root: Configurable, input: File, output: File): Zcat = {
+ val zcat = new Zcat(root)
+ zcat.input = input :: Nil
+ zcat.output = output
+ zcat
+ }
+
+ def apply(root: Configurable, input: List[File], output: File): Zcat = {
val zcat = new Zcat(root)
zcat.input = input
zcat.output = output
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 31c65252872c4ac3c01493bbf4ddc8abb6f5456e..5cbd73852e6a084a212a52052eebe1525bac3730 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -111,6 +111,6 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
required(reference) +
required(R1) +
optional(R2) +
- " > " + required(output)
+ (if (outputAsStsout) "" else " > " + required(output))
}
}
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
similarity index 97%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
index 2b4ebcc3866aad7fd2308f3b3d6755abadf5931b..144a91f21ae0479438fdb78f9432632d22584318 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
@@ -55,7 +55,7 @@ class CombineVariants(val root: Configurable) extends Gatk {
}
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
(for (file <- inputFiles) yield {
inputMap.get(file) match {
case Some(name) => required("-V:" + name, file)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
similarity index 95%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
index a738a17100d211623eb70648ca96081532432e9c..108253762bab534ab7740512da5ec692158dd0d4 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
@@ -49,6 +49,8 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
@Input(required = false)
var pedigree: List[File] = config("pedigree", default = Nil)
+ var et: Option[String] = config("et")
+
override def versionRegex = """(.*)""".r
override def versionExitcode = List(0, 1)
override def versionCommand = executable + " -jar " + jarFile + " -version"
@@ -61,10 +63,11 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
if (reference == null) reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-T", analysisType) +
required("-R", reference) +
optional("-K", gatkKey) +
+ optional("-et", et) +
repeat("-I", intervals) +
repeat("-XL", excludeIntervals) +
repeat("-ped", pedigree)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
index f2f7a1031a0892dc47605822f3a8f0ad1a656fdf..c9b30feeeb796c1b932c7aa61d4ccbd8a2c41837 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
@@ -64,7 +64,7 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
var RGPI: Option[Int] = _
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("SORT_ORDER=", sortOrder, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
similarity index 97%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
index 99f42e2b6e99f04c40880a2437bec242a386d672..5f3513fd7c22f0b81db0c739f6bb9b70237dc8d7 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
@@ -38,7 +38,7 @@ class BedToIntervalList(val root: Configurable) extends Picard with Reference {
@Output(doc = "Output interval list", required = true)
var output: File = null
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("SEQUENCE_DICTIONARY=", dict, spaceSeparated = false) +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index 23351a6459e283f4c5330e80a7a34918e6dd276a..ea7c37b5aef79dc59c942db3ae9127e90e853396 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -56,7 +56,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizabl
}
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
optional("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 7a02e7be2165472094085b1700f60d08d75b667c..ff19efe11676d2ca66adc172790080f9a9823783 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -53,7 +53,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
var stopAfter: Option[Long] = config("stopAfter")
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
optional("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 52ddd61758c50c27f7a3f8def6dc69f6815f4c9d..ada8007283b76122005cc5d4e6a0a39c161ea1aa 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -60,7 +60,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
}
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
optional("CHART_OUTPUT=", outputChart, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index b94b623c867019bf65d39987a796fa0808336b66..3c4693b5ead3929b9b1bf7eac95b69c3bed0c83c 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -62,7 +62,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
}
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
optional("HISTOGRAM_FILE=", outputHistogram, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
index 0ecc053022d3aaefdded69907d97618a891322d0..5ddaa72341c6a35b6cc9070c6d50cc48e80b7551 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
@@ -54,9 +54,6 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
@Argument(doc = "Stop after processing N reads", required = false)
var stopAfter: Option[Long] = config("stop_after")
- @Output
- protected var outputFiles: List[File] = Nil
-
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
@@ -79,7 +76,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
}
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", outputName, spaceSeparated = false) +
conditional(assumeSorted, "ASSUME_SORTED=true") +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 112c6afe42bbe93275d8713d74c330dc93b4bd5f..2aca96da6ebe993381766f50fc699c1c04233b0d 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -90,7 +90,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"metrics" -> Picard.getMetrics(output).getOrElse(Map()),
"histogram" -> Picard.getHistogram(output).getOrElse(Map()))
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("REF_FLAT=", refFlat, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
index 537ed3eea0eebfd88980bd41a29358591077e96a..7ec9598e98326dd1477a9d079bf4fe09b31e75af 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
@@ -60,7 +60,7 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard with Summ
if (reference == null) reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
index 97b429e3ff9c702fbe06b5efb07b6557b4ee44c9..6756f736623693564c344ca11da4a864d1c27977 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
@@ -62,7 +62,7 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
if (reference == null) reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
similarity index 96%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
index 0a7acc94375dc2457419ea82bd0730ad3ea63846..514c9394e8e6d8e663402cc03267fa70c6a2dc73 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
@@ -30,7 +30,7 @@ class GatherBamFiles(val root: Configurable) extends Picard {
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false)
}
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
similarity index 99%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index f7a77d20d459f8cbc8bfee32b12ece7e99d7a2eb..04a61ae0f9af329ac49252f93ccad829c60b7088 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -80,7 +80,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
}
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("METRICS_FILE=", outputMetrics, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index d358ba4e6b0d78c60a4d67d07f337be82750ea6f..5e90a5a625c992436a340a874bf60015c19b44ab 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -54,7 +54,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
}
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("SORT_ORDER=", sortOrder, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
similarity index 99%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index 9d00e0608818e3e76ece3eb9bfc35464fe3e0754..02678aac229d0113b19b8e2d3dfbb4eca53793ad 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -68,7 +68,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
else super.getVersion
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("TMP_DIR=" + jobTempDir) +
optional("VERBOSITY=", verbosity, spaceSeparated = false) +
conditional(quiet, "QUIET=TRUE") +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
similarity index 97%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
index c52d15d42e7a338ab0cb879ecf595f92bbe561ad..39a4fd184fdb73ea853e0b4a0419151773a377dc 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
@@ -45,7 +45,7 @@ class ReorderSam(val root: Configurable) extends Picard with Reference {
if (reference == null) reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
conditional(allowIncompleteDictConcordance, "ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE") +
conditional(allowContigLengthDiscordance, "ALLOW_CONTIG_LENGTH_DISCORDANCE=TRUE") +
required("REFERENCE=", reference, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
similarity index 98%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 6b26f48b8fafdcec9f79f39bd73d5c558f66f78f..b686e80225de8203af40b765764a0c1021e4446d 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -73,7 +73,7 @@ class SamToFastq(val root: Configurable) extends Picard {
var includeNonPrimaryAlignments: Boolean = config("includeNonPrimaryAlignments", default = false)
/** Returns command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("FASTQ=", fastqR1, spaceSeparated = false) +
optional("SECOND_END_FASTQ=", fastqR2, spaceSeparated = false) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
similarity index 77%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 078e794a5f14823e69b315c1f494efa4a1acc097..d9094ee5fa15c8caacd9a2c4823ccda7734c97e6 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -31,31 +31,32 @@ class SortSam(val root: Configurable) extends Picard {
var output: File = _
@Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
- var sortOrder: String = _
+ var sortOrder: String = config("sort_order", default = "coordinate")
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
override def beforeGraph() {
super.beforeGraph()
+ if (outputAsStsout) createIndex = false
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) +
+ override def cmdLine = super.cmdLine +
+ (if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
+ else required("INPUT=", input, spaceSeparated = false)) +
+ (if (outputAsStsout) required("OUTPUT=", new File("/dev/stdout"), spaceSeparated = false)
+ else required("OUTPUT=", output, spaceSeparated = false)) +
required("SORT_ORDER=", sortOrder, spaceSeparated = false)
}
object SortSam {
/** Returns default SortSam */
- def apply(root: Configurable, input: File, output: File, sortOrder: String = null): SortSam = {
+ def apply(root: Configurable, input: File, output: File): SortSam = {
val sortSam = new SortSam(root)
sortSam.input = input
sortSam.output = output
- if (sortOrder == null) sortSam.sortOrder = "coordinate"
- else sortSam.sortOrder = sortOrder
sortSam
}
}
\ No newline at end of file
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
new file mode 100644
index 0000000000000000000000000000000000000000..c8f9cf52007e9a74e344e3f78d74ec4ab1d2ac27
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -0,0 +1,37 @@
+package nl.lumc.sasc.biopet.extensions.samtools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+/**
+ * Created by pjvanthof on 22/09/15.
+ */
+class SamtoolsSort(val root: Configurable) extends Samtools {
+
+ @Input(required = true)
+ var input: File = _
+
+ @Output
+ var output: File = _
+
+ var compresion: Option[Int] = config("l")
+ var outputFormat: Option[String] = config("O")
+ var sortByName: Boolean = config("sort_by_name", default = false)
+ var prefix: String = _
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ prefix = config("prefix", default = new File(System.getProperty("java.io.tmpdir"), output.getName))
+ }
+
+ def cmdLine = required(executable) + required("sort") +
+ optional("-m", (coreMemeory + "G")) +
+ optional("-@", threads) +
+ optional("-O", outputFormat) +
+ required("-T", prefix) +
+ conditional(sortByName, "-n") +
+ (if (outputAsStsout) "" else required("-o", output)) +
+ (if (inputAsStdin) "" else required(input))
+}
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
similarity index 93%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
index 157f5d6500317b52dcaed70220d9eed5fd2bde4b..d69faa092303665a1c493686f3a1752010a9ef2a 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
@@ -25,14 +25,14 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Wrapper for the seqtk seq subcommand.
* Written based on seqtk version 1.0-r63-dirty.
*/
-class SeqtkSeq(val root: Configurable) extends Seqtk with Summarizable {
+class SeqtkSeq(val root: Configurable) extends Seqtk {
/** input file */
- @Input(doc = "Input file (FASTQ or FASTA)")
+ @Input(doc = "Input file (FASTQ or FASTA)", required = true)
var input: File = _
/** output file */
- @Output(doc = "Output file")
+ @Output(doc = "Output file", required = true)
var output: File = _
/** mask bases with quality lower than INT [0] */
@@ -106,8 +106,8 @@ class SeqtkSeq(val root: Configurable) extends Seqtk with Summarizable {
conditional(flag1, "-1") +
conditional(flag2, "-2") +
conditional(V, "-V") +
- required(input) +
- " > " + required(output)
+ (if (inputAsStdin) "" else required(input)) +
+ (if (outputAsStsout) "" else " > " + required(output))
}
/**
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
similarity index 96%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
index 773e466981ef703c8fc8f91b91b51b25b33d3054..0379c36d9ace680b7833bf226912504bb619f8e2 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
@@ -47,8 +47,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
variants.foreach { case v => require(validValues.contains(v), "variants value must be either 0 or 1") }
}
- override def commandLine = {
- val baseCommand = super.commandLine + required("mpileup2cns") +
+ override def cmdLine = {
+ val baseCommand = super.cmdLine + required("mpileup2cns") +
required("", input) +
required("--min-coverage", minCoverage) +
required("--min-reads2", minReads2) +
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
similarity index 100%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
diff --git a/public/biopet-extentsions/src/test/resources/log4j.properties b/public/biopet-extensions/src/test/resources/log4j.properties
similarity index 100%
rename from public/biopet-extentsions/src/test/resources/log4j.properties
rename to public/biopet-extensions/src/test/resources/log4j.properties
diff --git a/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics b/public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
similarity index 100%
rename from public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
rename to public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
diff --git a/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics b/public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
similarity index 100%
rename from public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
rename to public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
diff --git a/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics b/public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
similarity index 100%
rename from public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
rename to public/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
diff --git a/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
similarity index 100%
rename from public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
rename to public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
index 36770bb18747691afc468bf7cdff14d444478b81..b4109a45e70b0dd111463cddb3df7f2ebf74d14f 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
@@ -27,8 +27,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
nl.lumc.sasc.biopet.pipelines.carp.Carp,
nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
- nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling,
- nl.lumc.sasc.biopet.pipelines.gears.Gears
+ nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling
)
def pipelines: List[MainCommand] = List(
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
index 9b0020ae21e8626f3f987aaec2d1bd2921374bed..bc1d672269421ce7be6d64d15d0f8841c81332a1 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
@@ -55,7 +55,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with
reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
index bab2f7c0ae0fa260a78ff366d9e9f4a6c177d9f6..f7f00d0f94d43dcc45724c3ed4b61715072b88c1 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
@@ -38,7 +38,7 @@ class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 1.0
- override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
object BedToInterval {
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
index 817b6d3f2792168a8f4fdf8549fa3c16c858e21e..00a77a5e9d9ac4ec1e5c2d02ed350cdf53b10d5d 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
@@ -32,7 +32,7 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntio
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
index ff06bc963764f07563aa4ca0e2926119ba667c9b..5dc69cb07a34f04ed2cc32e7069875649c3aa32b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
@@ -37,7 +37,7 @@ class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Sum
override def defaultCoreMemory = 6.0
- override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
def summaryFiles: Map[String, File] = Map()
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
index df7e32e19bacfc8021ec015fcf019f9f16f61fe2..7348048447ca6c614b3b43ba915b228e042e9a37 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
@@ -37,7 +37,7 @@ class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
/** * Generate command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
repeat("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
index 90100c8e7942afe8dd105ca64ba2ff5990747b7f..f7829bb8e96cf7f09c318f61a59695d5c11a3a47 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, ToolCommandFuntion }
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -34,29 +34,34 @@ class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summariz
def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
- @Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
+ /** Original FASTQ file (read 1 or 2) */
+ @Input(required = true)
var refFastq: File = null
- @Input(doc = "Input read 1 FASTQ file", shortName = "i", required = true)
+ /** "Input read 1 FASTQ file" */
+ @Input(required = true)
var inputFastq1: File = null
- @Input(doc = "Input read 2 FASTQ file", shortName = "j", required = true)
+ /** Input read 2 FASTQ file */
+ @Input(required = true)
var inputFastq2: File = null
- @Output(doc = "Output read 1 FASTQ file", shortName = "o", required = true)
+ /** Output read 1 FASTQ file */
+ @Output(required = true)
var outputFastq1: File = null
- @Output(doc = "Output read 2 FASTQ file", shortName = "p", required = true)
+ /** Output read 2 FASTQ file */
+ @Output(required = true)
var outputFastq2: File = null
- @Output(doc = "Sync statistics", required = true)
+ /** Sync statistics */
+ @Output(required = true)
var outputStats: File = null
override def defaultCoreMemory = 4.0
- // executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-r", refFastq) +
required("-i", inputFastq1) +
required("-j", inputFastq2) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
index eedb51fdd1bb9d07d405299cb9dbf913681fbb96..504c7cb7c830cf8d1fa067b9048e7f23f4e3fe06 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
@@ -43,7 +43,7 @@ class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("-I", input) +
required("-o", output) +
required("-R", reference)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index 96a421db3e706d0220df76b6acfd5aab9cda9480..15ca55b6a524b283418ad67476d41b384541beb7 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -65,8 +65,8 @@ class MergeTables(val root: Configurable) extends ToolCommandFuntion {
var delimiter: Option[String] = config("delimiter")
// executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-i", idColumnIndices.mkString(",")) +
required("-a", valueColumnIndex) +
optional("-n", idColumnName) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index 5a3e1e3f26588c103a4bf5e0a190aa223d064450..60797ce9ca7f491a9dff0cf3a2379570cc6d91f5 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -57,7 +57,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
override def beforeCmd(): Unit = {
- if (sample == null && inputBam.exists()) {
+ if (sample == null && inputBam.exists() && inputBam.length() > 0) {
val inputSam = SamReaderFactory.makeDefault.open(inputBam)
val readGroups = inputSam.getFileHeader.getReadGroups
val samples = readGroups.map(readGroup => readGroup.getSample).distinct
@@ -66,14 +66,14 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
}
- override def commandLine = {
+ override def cmdLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
- super.commandLine +
+ super.cmdLine +
required("-o", output) +
optional("--minDP", minDP) +
optional("--minAP", minAP) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
index 302aa11586119a6602f29b0b452ed0645aeb2c37..dca36baf399c3f90725f61843ead5ed4416a08ab 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
@@ -44,7 +44,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
* Creates command to execute extension
* @return
*/
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-i", inputFastq) +
required("-o", outputFastq) +
optional("-s", prefixSeq)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index 2ee9d97e17ef35cbf6573bf0fa91bb5fc8f76b2c..0e71324dba7091729f044ff6b0815c04d5c937dd 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -32,7 +32,7 @@ class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
index 4b287d2cefaf98c777ca2ad44084f74bfacf5047..a2d79430f008d0a5818d98ae6ded6258ab74be0a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
@@ -44,7 +44,7 @@ class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
optional("--tag", tag) +
optional("--length", length) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
index d0779973b4484f29264bc574af6d898e1df8804d..30e7f524f65000789653085e4c6443a4e8a6d4a8 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
@@ -44,7 +44,7 @@ class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("--tagLib", tagLib) +
optional("--countSense", countSense) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
index cc7a8e6ede5bb1ba0d318639e8b9320a0ae8024a..3f1cf95a447f3f13827a27b82073fbf98e628495 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -24,7 +24,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
override def defaultCoreMemory = 2.5
- override def commandLine = super.commandLine + required("-i", input) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
index 558c93f8532b95ccd3dfa33e3265f0fbebda8104..f42f635be866d88fd92c9991c93f93afb9e880cd 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -20,7 +20,7 @@ class SquishBed(val root: Configurable) extends ToolCommandFuntion {
var strandSensitive: Boolean = config("strandSensitive", default = false)
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
conditional(strandSensitive, "-s")
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index 60d550532dfd30150e63f11096237356aa182a1a..06af56f025692658ad19c4e8375e7b81fbe599fc 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -38,7 +38,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
optional("--minSampleDepth", minSampleDepth) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 3fd09a67fb74b3759ec3f00c51344f88afc53231..d0024681b727e6f72fdc31da7483bb7b1c98b4f6 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -69,7 +69,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
}
/** Creates command to execute extension */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", outputDir) +
repeat("--infoTag", infoTags) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
index 5ab877502eaef6133b51a1927c83b94dc5b7b3ba..e956f5c93f5de3d9243de7bb5c9c1684de8f3fa4 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
@@ -50,7 +50,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
required("-s", secondaryVcf) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
index 4379b990dd585b012b15a44a7fc0605a7772b898..229f39628c9d1f8f8e23400b96a4fea957028e71 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
@@ -45,7 +45,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVCF) +
required("-O", outputVcf) +
required("-m", mode) +
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 4a08e55eca849eb40e0de7867f9504e83ac26cdb..f9646c4c9ebe7473e5ccb39e833d8ae87176b84a 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.ToolCommand
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import scala.collection.JavaConversions._
import scala.io.Source
@@ -52,8 +52,7 @@ object BedToInterval extends ToolCommand {
val writer = new PrintWriter(commandArgs.outputFile)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.bamFile)
- val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
- val record = SQ.asInstanceOf[SAMSequenceRecord]
+ val refs = for (record <- inputSam.getFileHeader.getSequenceDictionary.getSequences) yield {
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
record.getSequenceName -> record.getSequenceLength
}
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 960c4921debd6e58f45fa00bbb9dc0864dd11c60..62b04375f630ab59fea18d9c1d974bdf038cb767 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -625,6 +625,7 @@ object VcfStats extends ToolCommand {
def executeRscript(resource: String, args: Array[String]): Unit = {
val is = getClass.getResourceAsStream(resource)
val file = File.createTempFile("script.", "." + resource)
+ file.deleteOnExit()
val os = new FileOutputStream(file)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index ebe393bfab7bdb8fedec024319e99a5b0ec29a07..d9d8c1bee6bf96bcc98a372585b5a89454775e08 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -31,6 +31,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcf = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
@@ -40,6 +41,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcfAndBam = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
@@ -49,6 +51,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test def testMainVcfAndBamMore = {
val tmp = File.createTempFile("basty_out", ".fa")
+ tmp.deleteOnExit()
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
index 758cb6be6d6aa0a75c2ec1830e0fa3334beb7626..d919fe400154683f5fef7a061ce76c60aab5f5e7 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
@@ -56,6 +56,7 @@ class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
def testMain() = {
//TODO: Test output file
val output = File.createTempFile("testMain", ".biopetflagstat")
+ output.deleteOnExit()
main(Array("-I", bam.getAbsolutePath, "-o", output.toString))
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
index ffa8be0bcb6c2cf15bf0ad00efeeb54e903eb3df..dd66b204fab38a4fd26fb011ffe6739faf304009 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
@@ -23,7 +23,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
-
+ temp.deleteOnExit()
val args = Array("-I", fq, "-o", temp.getAbsolutePath)
main(args)
}
@@ -31,6 +31,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testManyOutMain() = {
val files = (0 until 10).map(_ => File.createTempFile("out", ".fastq"))
+ files.foreach(_.deleteOnExit())
var args = Array("-I", fq)
files.foreach(x => args ++= Array("-o", x.getAbsolutePath))
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
index b6de2f8bcca896e8979c2e21fc5bb8651524610a..907270b8c31f3eb152766f03a612101f754ba6c9 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -29,6 +29,7 @@ class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers
def testMain() = {
val outputFile = File.createTempFile("repeats", ".tsv")
+ outputFile.deleteOnExit()
val args = Array("-I", bam, "-b", bed, "-o", outputFile.toString)
main(args)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
index 032f9a913373c0f3be617e45cc26a928ca69821d..e708bc654b3c81699dcab85bfc07a7e21cd3ea94 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
@@ -28,6 +28,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath)
main(args)
@@ -36,6 +37,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def validateOutVcf() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
main(args)
@@ -51,6 +53,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def extraValidateOutVcf() = {
val tmp = File.createTempFile("mpileup", ".vcf")
+ tmp.deleteOnExit()
val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
index 41db9e3ae268a62860fd3fbe9a27e4430165429e..611557d836636aebc71f90e70707035033df6b97 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
@@ -26,6 +26,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
main(args)
@@ -34,6 +35,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testOutput() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
index 15d3074c95313c6f2a084c41b4d0a4787bdedddb..5c7731c6dd2ec60b7c8cd01f84c6929026d7e007 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
@@ -22,6 +22,7 @@ class SageCountFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
+ temp.deleteOnExit()
val args = Array("-I", fq, "-o", temp.getAbsolutePath)
main(args)
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
index 48038ea6f476fd89a945f53cf3d3608661fbcc9c..c86c1ba5a9787c0cdcce00293309500d6f6e4b86 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
@@ -29,9 +29,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
val input = resourcePath("/mini.transcriptome.fa")
val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ output.deleteOnExit()
val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ noTagsOutput.deleteOnExit()
val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ antiTagsOutput.deleteOnExit()
val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ allGenesOutput.deleteOnExit()
val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
"--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
@@ -52,9 +56,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
def testOutPut = {
val input = resourcePath("/mini.transcriptome.fa")
val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ output.deleteOnExit()
val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ noTagsOutput.deleteOnExit()
val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ antiTagsOutput.deleteOnExit()
val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ allGenesOutput.deleteOnExit()
val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
"--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
index b47c507856ec251878057a3823d47d57160045e9..ecd1dae87d5c43a88e722cbb12f7eb18ece3a9b8 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
@@ -26,9 +26,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val tagLib = resourcePath("/sageTest.tsv")
val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ sense.deleteOnExit()
val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allSense.deleteOnExit()
val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ antiSense.deleteOnExit()
val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allAntiSense.deleteOnExit()
noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
"--countSense", sense.getAbsolutePath, "--countAllSense", allSense.getAbsolutePath,
@@ -50,9 +54,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val tagLib = resourcePath("/sageTest.tsv")
val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ sense.deleteOnExit()
val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allSense.deleteOnExit()
val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ antiSense.deleteOnExit()
val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ allAntiSense.deleteOnExit()
main(Array("-I", input, "--tagLib", tagLib, "--countSense", sense.getAbsolutePath,
"--countAllSense", allSense.getAbsolutePath, "--countAntiSense", antiSense.getAbsolutePath,
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
index 9866ad47a8efbfad5f34868b82fe415f6e6b8c28..e8a09a9d7cb9af569f2084c95a1b6c2e7f1e1aad 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
@@ -21,6 +21,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testCorrectSampleTsv = {
val tsv = resourcePath("/sample.tsv")
val output = File.createTempFile("testCorrectSampleTsv", ".json")
+ output.deleteOnExit()
noException should be thrownBy main(Array("-i", tsv, "-o", output.toString))
}
@@ -29,6 +30,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testNoSampleColumn() = {
val tsv = resourcePath("/no_sample.tsv")
val output = File.createTempFile("testNoSampleColumn", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Sample column does not exist in: " + tsv)
}
@@ -37,6 +39,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testNumberInLibs = {
val tsv = resourcePath("/number.tsv")
val output = File.createTempFile("testNumberInLibs", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Sample or library may not start with a number")
}
@@ -45,6 +48,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def testSampleIDs = {
val tsv = resourcePath("/same.tsv")
val output = File.createTempFile("testSampleIDs", ".json")
+ output.deleteOnExit()
val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
thrown.getMessage should equal("Combination of Sample_ID_1 and Lib_ID_1 is found multiple times")
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
index 6071fceaaed85a943a4f973ac713d24e8b708952..4f921affbc090031b83c0ee5fea3c64b9c9bdf4c 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -24,6 +24,7 @@ class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
def testMain = {
val tsv = resourcePath("/test.summary.json")
val output = File.createTempFile("main", "tsv")
+ output.deleteOnExit()
noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
"-m", "root", "-o", output.toString))
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index af8ff6267d5c73dad9eaa10762b1d356a2641626..a6a70881012480a8e92b9aac1c689e4456f9f8c7 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -47,50 +47,57 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testOutputTypeVcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf.gz").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeBcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".bcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputFieldException = {
- val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:AC")
+ val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:AC")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Field 'AC' already exists in input vcf")
}
@Test def testInputFieldException = {
- val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpPath, "-f", "CSQ:NEW_CSQ")
+ val tmpFile = File.createTempFile("VCFWithVCf", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:NEW_CSQ")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Field 'CSQ' does not exist in secondary vcf")
}
@Test def testMinMethodException = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:min")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:min")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Type of field CSQ is not numeric")
}
@Test def testMaxMethodException = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:max")
+ val tmpFile = File.createTempFile("VcfWithVcf_", ".vcf")
+ tmpFile.deleteOnExit()
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpFile.getAbsolutePath, "-f", "CSQ:CSQ:max")
an[IllegalArgumentException] should be thrownBy main(args)
val thrown = the[IllegalArgumentException] thrownBy main(args)
thrown.getMessage should equal("Type of field CSQ is not numeric")
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index 5a12e9b579296b58a2764fdaa0b5b916717e384f..53aeddfaf1d6ba87f9e89ac29b31edff8fc5e01b 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -47,38 +47,44 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testGzOutputExplode(): Unit = {
- val tmpPath = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testVcfOutputExplode(): Unit = {
- val tmpPath = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testBcfOutputExplode(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testGzOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testVcfOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testBcfOutputStandard(): Unit = {
- val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+ val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
+ tmpFile.deleteOnExit()
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
index fb0e2f0a0706a56c6063c2a2fa2dc199bfee573c..1954609198b33dcaa380eaafa3534f463ef43d4c 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
@@ -48,5 +48,5 @@ class LinePlot(val root: Configurable) extends Rscript {
ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
title.map(Seq("--title", _)).getOrElse(Seq()) ++
- (if (removeZero) Seq("--removeZero") else Seq())
+ (if (removeZero) Seq("--removeZero", "true") else Seq())
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
index 685108d0cb7f31cebfcc4b998017ae0a4c91726f..3dfac894eeb591a84a31b3fd5bcfa88c34619192 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
@@ -28,7 +28,11 @@ trait Rscript extends Configurable {
} else {
val rScript: File = dir match {
case Some(dir) => new File(dir, script.getName)
- case _ => File.createTempFile(script.getName, ".R")
+ case _ => {
+ val file = File.createTempFile(script.getName, ".R")
+ file.deleteOnExit()
+ file
+ }
}
if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index ad8ff00ee2e8a09026168efbf99f5926b4583c50..6bac74cdf9f3bf6148a78b05271593242d9b2d07 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -228,6 +228,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
object ConfigUtilsTest {
def writeTemp(text: String, extension: String): File = {
val file = File.createTempFile("TestConfigUtils.", extension)
+ file.deleteOnExit()
val w = new PrintWriter(file)
w.write(text)
w.close()
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
index b748006c2800d5e86aad9e5f918a3d4bf5894c2c..0490b28db7dbf199a9b01c1b48c6783f11720f7d 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
@@ -39,6 +39,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records.header shouldBe Nil
val tempFile = File.createTempFile("region", ".bed")
+ tempFile.deleteOnExit()
records.writeToFile(tempFile)
BedRecordList.fromFile(tempFile) shouldBe records
tempFile.delete()
@@ -50,6 +51,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records.header shouldBe BedRecordListTest.ucscHeader.split("\n").toList
val tempFile = File.createTempFile("region", ".bed")
+ tempFile.deleteOnExit()
records.writeToFile(tempFile)
BedRecordList.fromFile(tempFile) shouldBe records
tempFile.delete()
@@ -129,13 +131,6 @@ class BedRecordListTest extends TestNGSuite with Matchers {
list.scatter(100).allRecords.size shouldBe 15
list.scatter(100).length shouldBe 1500
}
-
- @AfterClass
- def end: Unit = {
- BedRecordListTest.bedFile.delete()
- BedRecordListTest.corruptBedFile.delete()
- BedRecordListTest.bedFileUcscHeader.delete()
- }
}
object BedRecordListTest {
@@ -149,6 +144,9 @@ object BedRecordListTest {
|chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399 0,3601""".stripMargin
val bedFile = File.createTempFile("regions", ".bed")
+ bedFile.deleteOnExit()
val corruptBedFile = File.createTempFile("regions", ".bed")
+ corruptBedFile.deleteOnExit()
val bedFileUcscHeader = File.createTempFile("regions", ".bed")
+ bedFileUcscHeader.deleteOnExit()
}
\ No newline at end of file
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 1233eecd6cf1c49d7f57ae27b398d8998b8c3494..71b51067a73baaf49c7d1a095d13d1fa584e7e96 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -78,6 +78,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
if (config.contains("R1")) {
mapping.input_R1 = config("R1")
if (config.contains("R2")) mapping.input_R2 = config("R2")
+
+ inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+ mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
+
mapping.init()
mapping.biopetScript()
addAll(mapping.functions)
@@ -107,7 +111,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
add(merge)
}
- val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"))
+ val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
addAll(Bam2Wig(qscript, bamFile).functions)
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
index c5f2256b0c4cf7c4815c305bab8907573449c5a4..59a07dca040ff07f81438b59697953563b97d972 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
@@ -76,7 +76,7 @@ object CarpReport extends MultisampleReportBuilder {
), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
- "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
+ "Merged" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args)
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index c361908fa1110ef7133639e91912acab5cce0da9..1f5efdc2fb950dfca40e7a870bba7da984db0c41 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -81,8 +81,8 @@ class CarpTest extends TestNGSuite with Matchers {
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0) +
(if (threatment) 1 else 0) + (if (control) 1 else 0)
- carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
- carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
+ //carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
+ //carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
carp.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (sample3) 1 else 0)
carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
@@ -97,6 +97,12 @@ class CarpTest extends TestNGSuite with Matchers {
object CarpTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -127,8 +133,8 @@ object CarpTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -136,8 +142,8 @@ object CarpTest {
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
)
)
)))
@@ -145,12 +151,12 @@ object CarpTest {
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("3_1_R1.fq"),
+ "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("3_2_R1.fq"),
+ "R2" -> inputTouch("3_2_R2.fq")
)
)
)))
@@ -158,8 +164,8 @@ object CarpTest {
val threatment1 = Map(
"samples" -> Map("threatment" -> Map("control" -> "control1", "libraries" -> Map(
"lib1" -> Map(
- "R1" -> "threatment_1_R1.fq",
- "R2" -> "threatment_1_R2.fq"
+ "R1" -> inputTouch("threatment_1_R1.fq"),
+ "R2" -> inputTouch("threatment_1_R2.fq")
)
)
)))
@@ -167,8 +173,8 @@ object CarpTest {
val control1 = Map(
"samples" -> Map("control1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "control_1_R1.fq",
- "R2" -> "control_1_R2.fq"
+ "R1" -> inputTouch("control_1_R1.fq"),
+ "R2" -> inputTouch("control_1_R2.fq")
)
)
)))
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
index c327a7cef9b16719f1ec4be35ee556005c9bee2e..b2f0057b3dc437c496c4a161af515c11f9a3d80e 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
@@ -129,7 +129,7 @@
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).toString.toLong
- val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).toString.toLong
+ val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "bases", "num_total").getOrElse(0).toString.toLong
}#
<td>${read}</td>
<td>${beforeTotal}</td>
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
index 17065bb987d62f147e76a3c096f3db0847bcd265..4a0a60659f5276f7230fef7fabd4cc12f23ae4a4 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
@@ -133,7 +133,7 @@
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
- val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
+ val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total")
val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).toString.toLong
val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).toString.toLong
val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).toString.toLong
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
deleted file mode 100644
index 63301b52ad02ad124ac820e791a1de4d385505d3..0000000000000000000000000000000000000000
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ /dev/null
@@ -1,87 +0,0 @@
-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.pipelines.flexiprep
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
-
-import scala.collection.mutable
-import scala.io.Source
-
-class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
- var fastqc: Fastqc = _
-
- override def beforeCmd() {
- super.beforeCmd()
-
- val foundAdapters = fastqc.foundAdapters.map(_.seq)
- if (default_clip_mode == "3") opt_adapter ++= foundAdapters
- else if (default_clip_mode == "5") opt_front ++= foundAdapters
- else if (default_clip_mode == "both") opt_anywhere ++= foundAdapters
- }
-
- override def summaryStats: Map[String, Any] = {
- val trimR = """.*Trimmed reads: *(\d*) .*""".r
- val tooShortR = """.*Too short reads: *(\d*) .*""".r
- val tooLongR = """.*Too long reads: *(\d*) .*""".r
- val adapterR = """Adapter '([C|T|A|G]*)'.*trimmed (\d*) times.""".r
-
- val stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
- val adapter_stats: mutable.Map[String, List[Any]] = mutable.Map()
-
- if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines()) {
- line match {
- case trimR(m) => stats += ("trimmed" -> m.toInt)
- case tooShortR(m) => stats += ("tooshort" -> m.toInt)
- case tooLongR(m) => stats += ("toolong" -> m.toInt)
- case adapterR(adapter, count) =>
- val adapterName = fastqc.foundAdapters.find(_.seq == adapter) match {
- case None => "unknown"
- case Some(a) => a.name
- }
- adapter_stats += (adapterName -> List(adapter, count.toInt))
- case _ =>
- }
- }
-
- Map("num_reads_affected" -> stats("trimmed"),
- "num_reads_discarded_too_short" -> stats("tooshort"),
- "num_reads_discarded_too_long" -> stats("toolong"),
- "adapters" -> adapter_stats.toMap
- )
- }
- override def cmdLine = {
- if (opt_adapter.nonEmpty || opt_anywhere.nonEmpty || opt_front.nonEmpty) {
- analysisName = getClass.getSimpleName
- super.cmdLine
- } else {
- analysisName = getClass.getSimpleName + "-ln"
- Ln(this, fastq_input, fastq_output, relative = true).cmd
- }
- }
-}
-
-object Cutadapt {
- def apply(root: Configurable, input: File, output: File): Cutadapt = {
- val cutadapt = new Cutadapt(root)
- cutadapt.fastq_input = input
- cutadapt.fastq_output = output
- cutadapt.stats_output = new File(output.getAbsolutePath.substring(0, output.getAbsolutePath.lastIndexOf(".")) + ".stats")
- cutadapt
- }
-}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 60fe0da7fbdf0f2ac24ee08bd929c7b66bdaf164..6c444bed885b3b4219728bf38423156b3d545064 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -181,9 +181,6 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
} else Set()
}
- @Output
- var outputFiles: List[File] = Nil
-
def summaryFiles: Map[String, File] = {
val outputFiles = Map("plot_duplication_levels" -> ("Images" + File.separator + "duplication_levels.png"),
"plot_kmer_profiles" -> ("Images" + File.separator + "kmer_profiles.png"),
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 16362f9e1ee2010b549ff82728934330f85925cd..aeab29b7d697093726674b263f916faf77bccd7d 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -16,10 +16,10 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
-import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -45,11 +45,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def summaryFiles: Map[String, File] = {
- if (!skipTrim || !skipClip)
- Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
- (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
- else Map("input_R1" -> input_R1) ++
- (if (paired) Map("input_R2" -> input_R2.get) else Map())
+ Map("input_R1" -> input_R1, "output_R1" -> fastqR1Qc) ++
+ (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> fastqR2Qc.get) else Map())
}
/** returns settings to store in summary */
@@ -85,6 +82,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
paired = input_R2.isDefined
+ inputFiles :+= new InputFile(input_R1)
+ input_R2.foreach(inputFiles :+= new InputFile(_))
+
if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
else R1_name = input_R1.getName
@@ -107,8 +107,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def biopetScript() {
runInitialJobs()
- val out = if (paired) runTrimClip(outputFiles("fastq_input_R1"), Some(outputFiles("fastq_input_R2")), outputDir)
- else runTrimClip(outputFiles("fastq_input_R1"), outputDir)
+ if (paired) runTrimClip(input_R1, input_R2, outputDir)
+ else runTrimClip(input_R1, outputDir)
val R1_files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
val R2_files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
@@ -117,8 +117,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Add init non chunkable jobs */
def runInitialJobs() {
- outputFiles += ("fastq_input_R1" -> extractIfNeeded(input_R1, outputDir))
- if (paired) outputFiles += ("fastq_input_R2" -> extractIfNeeded(input_R2.get, outputDir))
+ outputFiles += ("fastq_input_R1" -> input_R1)
+ if (paired) outputFiles += ("fastq_input_R2" -> input_R2.get)
fastqc_R1 = Fastqc(this, input_R1, new File(outputDir, R1_name + ".fastqc/"))
add(fastqc_R1)
@@ -131,9 +131,26 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable(fastqc_R2, "fastqc_R2")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
}
+
+ val seqstat_R1 = SeqStat(this, input_R1, outputDir)
+ seqstat_R1.isIntermediate = true
+ add(seqstat_R1)
+ addSummarizable(seqstat_R1, "seqstat_R1")
+
+ if (paired) {
+ val seqstat_R2 = SeqStat(this, input_R2.get, outputDir)
+ seqstat_R2.isIntermediate = true
+ add(seqstat_R2)
+ addSummarizable(seqstat_R2, "seqstat_R2")
+ }
}
- //TODO: Refactor need to combine all this functions
+ def fastqR1Qc = if (paired)
+ new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.sync.fq.gz")
+ else new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.fq.gz")
+ def fastqR2Qc = if (paired)
+ Some(new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R2.qc.sync.fq.gz"))
+ else None
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, Option[File], List[File]) =
@@ -150,111 +167,75 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File, chunkarg: String): (File, Option[File], List[File]) = {
val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_"
- var results: Map[String, File] = Map()
var R1 = R1_in
var R2 = R2_in
- var deps_R1 = R1 :: Nil
- var deps_R2 = if (paired) R2.get :: Nil else Nil
- def deps: List[File] = deps_R1 ::: deps_R2
-
- val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
- seqtkSeq_R1.isIntermediate = true
- add(seqtkSeq_R1)
- addSummarizable(seqtkSeq_R1, "seqtkSeq_R1")
- R1 = seqtkSeq_R1.output
- deps_R1 ::= R1
-
- if (paired) {
- val seqtkSeq_R2 = SeqtkSeq(this, R2.get, swapExt(outDir, R2.get, R2_ext, ".sanger" + R2_ext), fastqc_R2)
- seqtkSeq_R2.isIntermediate = true
- add(seqtkSeq_R2)
- addSummarizable(seqtkSeq_R2, "seqtkSeq_R2")
- R2 = Some(seqtkSeq_R2.output)
- deps_R2 ::= R2.get
- }
+ def deps: List[File] = Nil
- val seqstat_R1 = SeqStat(this, R1, outDir)
- seqstat_R1.isIntermediate = true
- seqstat_R1.deps = deps_R1
- add(seqstat_R1)
- addSummarizable(seqstat_R1, "seqstat_R1")
+ val qcCmdR1 = new QcCommand(this, fastqc_R1)
+ qcCmdR1.input = R1_in
+ qcCmdR1.read = "R1"
+ qcCmdR1.output = if (paired) new File(fastqR1Qc.getAbsolutePath.stripSuffix(".gz"))
+ else fastqR1Qc
+ qcCmdR1.deps :+= fastqc_R1.output
+ qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
+ addSummarizable(qcCmdR1, "qc_command_R1")
if (paired) {
- val seqstat_R2 = SeqStat(this, R2.get, outDir)
- seqstat_R2.isIntermediate = true
- seqstat_R2.deps = deps_R2
- add(seqstat_R2)
- addSummarizable(seqstat_R2, "seqstat_R2")
- }
-
- if (!skipClip) { // Adapter clipping
-
- val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
- cutadapt_R1.fastqc = fastqc_R1
- cutadapt_R1.isIntermediate = true
- cutadapt_R1.deps = deps_R1
- add(cutadapt_R1)
- addSummarizable(cutadapt_R1, "clipping_R1")
- R1 = cutadapt_R1.fastq_output
- deps_R1 ::= R1
- outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
-
- if (paired) {
- val cutadapt_R2 = Cutadapt(this, R2.get, swapExt(outDir, R2.get, R2_ext, ".clip" + R2_ext))
- outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
- cutadapt_R2.fastqc = fastqc_R2
- cutadapt_R2.isIntermediate = true
- cutadapt_R2.deps = deps_R2
- add(cutadapt_R2)
- addSummarizable(cutadapt_R2, "clipping_R2")
- R2 = Some(cutadapt_R2.fastq_output)
- deps_R2 ::= R2.get
-
- val fqSync = new FastqSync(this)
- fqSync.refFastq = cutadapt_R1.fastq_input
- fqSync.inputFastq1 = cutadapt_R1.fastq_output
- fqSync.inputFastq2 = cutadapt_R2.fastq_output
- fqSync.outputFastq1 = swapExt(outDir, R1, R1_ext, ".sync" + R1_ext)
- fqSync.outputFastq2 = swapExt(outDir, R2.get, R2_ext, ".sync" + R2_ext)
- fqSync.outputStats = swapExt(outDir, R1, R1_ext, ".sync.stats")
- fqSync.deps :::= deps
- add(fqSync)
- addSummarizable(fqSync, "fastq_sync")
- outputFiles += ("syncStats" -> fqSync.outputStats)
- R1 = fqSync.outputFastq1
- R2 = Some(fqSync.outputFastq2)
- deps_R1 ::= R1
- deps_R2 ::= R2.get
+ val qcCmdR2 = new QcCommand(this, fastqc_R2)
+ qcCmdR2.input = R2_in.get
+ qcCmdR2.output = new File(fastqR2Qc.get.getAbsolutePath.stripSuffix(".gz"))
+ qcCmdR2.read = "R2"
+ addSummarizable(qcCmdR2, "qc_command_R2")
+
+ qcCmdR1.compress = false
+ qcCmdR2.compress = false
+
+ val fqSync = new FastqSync(this)
+ fqSync.refFastq = R1_in
+ fqSync.inputFastq1 = qcCmdR1.output
+ fqSync.inputFastq2 = qcCmdR2.output
+ fqSync.outputFastq1 = fastqR1Qc
+ fqSync.outputFastq2 = fastqR2Qc.get
+ fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
+
+ val pipe = new BiopetFifoPipe(this, fqSync :: Nil) {
+ override def configName = "qc-cmd"
+
+ override def beforeGraph(): Unit = {
+ fqSync.beforeGraph()
+ super.beforeGraph()
+ }
+
+ override def beforeCmd(): Unit = {
+ qcCmdR1.beforeCmd()
+ qcCmdR2.beforeCmd()
+ fqSync.beforeCmd()
+ commands = qcCmdR1.jobs ::: qcCmdR2.jobs ::: fqSync :: Nil
+ super.beforeCmd()
+ }
}
- }
- if (!skipTrim) { // Quality trimming
- val sickle = new Sickle(this)
- sickle.input_R1 = R1
- sickle.output_R1 = swapExt(outDir, R1, R1_ext, ".trim" + R1_ext)
- if (paired) {
- sickle.input_R2 = R2.get
- sickle.output_R2 = swapExt(outDir, R2.get, R2_ext, ".trim" + R2_ext)
- sickle.output_singles = swapExt(outDir, R2.get, R2_ext, ".trim.singles" + R1_ext)
- }
- sickle.output_stats = swapExt(outDir, R1, R1_ext, ".trim.stats")
- sickle.deps = deps
- sickle.isIntermediate = true
- add(sickle)
- addSummarizable(sickle, "trimming")
- R1 = sickle.output_R1
- if (paired) R2 = Some(sickle.output_R2)
+ pipe.deps ::= fastqc_R1.output
+ pipe.deps ::= fastqc_R2.output
+ pipe.isIntermediate = !keepQcFastqFiles
+ add(pipe)
+
+ addSummarizable(fqSync, "fastq_sync")
+ outputFiles += ("syncStats" -> fqSync.outputStats)
+ R1 = fqSync.outputFastq1
+ R2 = Some(fqSync.outputFastq2)
+ } else {
+ add(qcCmdR1)
+ R1 = qcCmdR1.output
}
val seqstat_R1_after = SeqStat(this, R1, outDir)
- seqstat_R1_after.deps = deps_R1
add(seqstat_R1_after)
addSummarizable(seqstat_R1_after, "seqstat_R1_qc")
if (paired) {
val seqstat_R2_after = SeqStat(this, R2.get, outDir)
- seqstat_R2_after.deps = deps_R2
add(seqstat_R2_after)
addSummarizable(seqstat_R2_after, "seqstat_R2_qc")
}
@@ -266,23 +247,24 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Adds last non chunkable jobs */
def runFinalize(fastq_R1: List[File], fastq_R2: List[File]) {
- if (fastq_R1.length != fastq_R2.length && paired) throw new IllegalStateException("R1 and R2 file number is not the same")
- val R1 = new File(outputDir, R1_name + ".qc" + R1_ext + ".gz")
- val R2 = new File(outputDir, R2_name + ".qc" + R2_ext + ".gz")
+ if (fastq_R1.length != fastq_R2.length && paired)
+ throw new IllegalStateException("R1 and R2 file number is not the same")
if (!skipTrim || !skipClip) {
- add(Gzip(this, fastq_R1, R1), !keepQcFastqFiles)
- if (paired) add(Gzip(this, fastq_R2, R2), !keepQcFastqFiles)
+ if (fastq_R1.length > 1) {
+ add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
+ if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
+ }
- outputFiles += ("output_R1_gzip" -> R1)
- if (paired) outputFiles += ("output_R2_gzip" -> R2)
+ outputFiles += ("output_R1_gzip" -> fastqR1Qc)
+ if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
- fastqc_R1_after = Fastqc(this, R1, new File(outputDir, R1_name + ".qc.fastqc/"))
+ fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
add(fastqc_R1_after)
addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
if (paired) {
- fastqc_R2_after = Fastqc(this, R2, new File(outputDir, R2_name + ".qc.fastqc/"))
+ fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
add(fastqc_R2_after)
addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
}
@@ -290,25 +272,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummaryJobs()
}
-
- /** Extracts file if file is compressed */
- def extractIfNeeded(file: File, runDir: File): File = {
- if (file == null) 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)
- newFile
- } else if (file.getName.endsWith(".bz2")) {
- val newFile = swapExt(runDir, file, ".bz2", "")
- val pbzip2 = Pbzip2(this, file, newFile)
- pbzip2.isIntermediate = true
- add(pbzip2)
- newFile
- } else file
- }
}
object Flexiprep extends PipelineCommand
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
index c4988cd1e1b131a98d2d4dc52086fef58085e1bc..075077872a314c2a510478ff8a151a4ed7f5ba9c 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
@@ -95,7 +95,7 @@ object FlexiprepReport extends ReportBuilder {
def getLine(summary: Summary, sample: String, lib: String): String = {
val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "reads", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
- val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total"),
+ val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val clippingDiscardedToShort = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
@@ -152,7 +152,7 @@ object FlexiprepReport extends ReportBuilder {
def getLine(summary: Summary, sample: String, lib: String): String = {
val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "bases", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
- val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total"),
+ val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_qc", "bases", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val sb = new StringBuffer()
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3e516b638398f008435c5c5a982e09efcc335a86
--- /dev/null
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -0,0 +1,144 @@
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction, BiopetPipe }
+import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
+import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 9/22/15.
+ */
+class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetCommandLineFunction with Summarizable {
+
+ val flexiprep = root match {
+ case f: Flexiprep => f
+ case _ => throw new IllegalArgumentException("This class may only be used inside Flexiprep")
+ }
+
+ @Input(required = true)
+ var input: File = _
+
+ @Output(required = true)
+ var output: File = _
+
+ var compress = true
+
+ var read: String = _
+
+ override def defaultCoreMemory = 2.0
+ override def defaultThreads = 3
+
+ val seqtk = new SeqtkSeq(root)
+ var clip: Option[Cutadapt] = None
+ var trim: Option[Sickle] = None
+ var outputCommand: BiopetCommandLineFunction = null
+
+ def jobs = (Some(seqtk) :: clip :: trim :: Some(outputCommand) :: Nil).flatten
+
+ def summaryFiles = Map()
+
+ def summaryStats = Map()
+
+ override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
+ clip match {
+ case Some(job) => qscript.addSummarizable(job, s"clipping_$read")
+ case _ =>
+ }
+ trim match {
+ case Some(job) => qscript.addSummarizable(job, s"trimming_$read")
+ case _ =>
+ }
+ }
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ require(read != null)
+ deps ::= input
+ outputFiles :+= output
+ }
+
+ override def beforeCmd(): Unit = {
+ seqtk.input = input
+ seqtk.output = new File(output.getParentFile, input.getName + ".seqtk.fq")
+ seqtk.Q = fastqc.encoding match {
+ case null => None
+ case enc if enc.contains("Sanger / Illumina 1.9") => None
+ case enc if enc.contains("Illumina <1.3") => Option(64)
+ case enc if enc.contains("Illumina 1.3") => Option(64)
+ case enc if enc.contains("Illumina 1.5") => Option(64)
+ case _ => None
+ }
+ if (seqtk.Q.isDefined) seqtk.V = true
+
+ clip = if (!flexiprep.skipClip) {
+ val foundAdapters = fastqc.foundAdapters.map(_.seq)
+ if (foundAdapters.nonEmpty) {
+ val cutadept = new Cutadapt(root)
+ cutadept.fastq_input = seqtk.output
+ cutadept.fastq_output = new File(output.getParentFile, input.getName + ".cutadept.fq")
+ cutadept.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
+ if (cutadept.default_clip_mode == "3") cutadept.opt_adapter ++= foundAdapters
+ else if (cutadept.default_clip_mode == "5") cutadept.opt_front ++= foundAdapters
+ else if (cutadept.default_clip_mode == "both") cutadept.opt_anywhere ++= foundAdapters
+ Some(cutadept)
+ } else None
+ } else None
+
+ trim = if (!flexiprep.skipTrim) {
+ val sickle = new Sickle(root)
+ sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
+ sickle.input_R1 = clip match {
+ case Some(clip) => clip.fastq_output
+ case _ => seqtk.output
+ }
+ sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
+ Some(sickle)
+ } else None
+
+ val outputFile = (clip, trim) match {
+ case (_, Some(trim)) => trim.output_R1
+ case (Some(clip), _) => clip.fastq_output
+ case _ => seqtk.output
+ }
+
+ if (compress) outputCommand = {
+ val gzip = new Gzip(root)
+ gzip.output = output
+ outputFile :<: gzip
+ }
+ else outputCommand = {
+ val cat = new Cat(root)
+ cat.input = outputFile :: Nil
+ cat.output = output
+ cat
+ }
+
+ seqtk.beforeGraph()
+ clip.foreach(_.beforeGraph())
+ trim.foreach(_.beforeGraph())
+ outputCommand.beforeGraph()
+
+ seqtk.beforeCmd()
+ clip.foreach(_.beforeCmd())
+ trim.foreach(_.beforeCmd())
+ outputCommand.beforeCmd()
+ }
+
+ def cmdLine = {
+
+ val cmd = (clip, trim) match {
+ case (Some(clip), Some(trim)) => new BiopetFifoPipe(root, seqtk :: clip :: trim :: outputCommand :: Nil)
+ case (Some(clip), _) => new BiopetFifoPipe(root, seqtk :: clip :: outputCommand :: Nil)
+ case (_, Some(trim)) => new BiopetFifoPipe(root, seqtk :: trim :: outputCommand :: Nil)
+ case _ => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
+ }
+
+ //val cmds = (Some(seqtk) :: clip :: trim :: Some(new Gzip(root)) :: Nil).flatten
+ cmd.beforeGraph()
+ cmd.commandLine
+ }
+}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
deleted file mode 100644
index 2105a3c4a2dbc1d2a563c35a6b5e92d752bbefeb..0000000000000000000000000000000000000000
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ /dev/null
@@ -1,65 +0,0 @@
-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.pipelines.flexiprep
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
-
-class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
- var fastqc: Fastqc = _
-
- override def beforeCmd() {
- super.beforeCmd()
- if (fastqc != null && Q.isEmpty) {
- val encoding = fastqc.encoding
- Q = encoding match {
- case null => None
- case enc if enc.contains("Sanger / Illumina 1.9") => None
- case enc if enc.contains("Illumina <1.3") => Option(64)
- case enc if enc.contains("Illumina 1.3") => Option(64)
- case enc if enc.contains("Illumina 1.5") => Option(64)
- case _ => None
- }
- if (Q.isDefined) V = true
- }
- }
-
- override def beforeGraph() {
- if (fastqc != null) deps ::= fastqc.output
- }
-
- override def cmdLine = {
- if (Q.isDefined) {
- analysisName = getClass.getSimpleName
- super.cmdLine
- } else {
- analysisName = getClass.getSimpleName + "-ln"
- Ln(this, input, output).cmd
- }
- }
-}
-
-object SeqtkSeq {
- def apply(root: Configurable, input: File, output: File, fastqc: Fastqc = null): SeqtkSeq = {
- val seqtkSeq = new SeqtkSeq(root)
- seqtkSeq.input = input
- seqtkSeq.output = output
- seqtkSeq.fastqc = fastqc
- seqtkSeq
- }
-}
\ No newline at end of file
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 2cb3f0e7b36175d9bf7633d7d639e6b03612976f..f7f9dc2ab2d916e22c0a6858663f1a43773f7f22 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -67,8 +67,8 @@ class FlexiprepTest extends TestNGSuite with Matchers {
), Map(FlexiprepTest.executables.toSeq: _*))
val flexiprep: Flexiprep = initPipeline(map)
- flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
- if (paired) flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq" + (if (zipped) ".gz" else "")))
+ flexiprep.input_R1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
+ if (paired) flexiprep.input_R2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
flexiprep.sampleId = Some("1")
flexiprep.libId = Some("1")
flexiprep.script()
@@ -79,12 +79,6 @@ class FlexiprepTest extends TestNGSuite with Matchers {
else if (paired && !(skipClip && skipTrim)) 4
else if (!paired && !(skipClip && skipTrim)) 2)
flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
- flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) if (paired) 2 else 1 else 0)
- flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
- flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
- flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else if (paired) 1 else 0)
- flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
- flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipClip && skipTrim) 0 else if (paired) 2 else 1)
}
// remove temporary run directory all tests in the class have been run
@@ -95,6 +89,16 @@ class FlexiprepTest extends TestNGSuite with Matchers {
object FlexiprepTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+ Files.touch(r1)
+ val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+ Files.touch(r2)
+ val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
+ Files.touch(r1Zipped)
+ val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+ Files.touch(r2Zipped)
val executables = Map(
"seqstat" -> Map("exe" -> "test"),
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 6ae0e69bb4410870b79e91731ff3c98f89f44445..724470df1091228bbdaf928b49ae7024f2bb70bd 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -843,6 +843,8 @@ class Gentrap(val root: Configurable) extends QScript
def addJobs(): Unit = {
// create per-library alignment file
addAll(mappingJob.functions)
+ // Input file checking
+ inputFiles :::= mappingJob.inputFiles
// add bigwig track
addAll(bam2wigModule.functions)
qscript.addSummaryQScript(mappingJob)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index 1ce8465cae9c75dbcbed9c85374074202ff9b393..8871f481f3075d7eef52784583ccb5aadaa5b715 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
@@ -28,16 +28,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
// FIXME: generalize piping instead of building something by hand like this!
// Better to do everything quick and dirty here rather than something half-implemented with the objects
-class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction { wrapper =>
+class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction with Reference { wrapper =>
override def configName = "customvarscan"
@Input(doc = "Input BAM file", required = true)
var input: File = null
- @Input(doc = "Reference FASTA file", required = true)
- var reference: File = config("reference")
-
@Output(doc = "Output VCF file", required = true)
var output: File = null
@@ -49,7 +46,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
this.input = List(wrapper.input)
override def configName = wrapper.configName
disableBaq = true
- reference = config("reference")
depth = Option(1000000)
outputMappingQuality = true
}
@@ -92,7 +88,9 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
}
override def beforeGraph(): Unit = {
+ super.beforeGraph()
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
+ deps :+= referenceFasta()
}
def cmdLine: String = {
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 140db66fd62dd850365b27137cc3df0891bd38a7..2b2ddaf259e8fa5ad382ef1aca1337826ecf0ad8 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -43,8 +43,8 @@ class GentrapTest extends TestNGSuite with Matchers {
/** Convenience method for making library config */
private def makeLibConfig(idx: Int, paired: Boolean = true) = {
- val files = Map("R1" -> "test_R1.fq")
- if (paired) (s"lib_$idx", files ++ Map("R2" -> "test_R2.fq"))
+ val files = Map("R1" -> GentrapTest.inputTouch("test_R1.fq"))
+ if (paired) (s"lib_$idx", files ++ Map("R2" -> GentrapTest.inputTouch("test_R2.fq")))
else (s"lib_$idx", files)
}
@@ -179,6 +179,12 @@ class GentrapTest extends TestNGSuite with Matchers {
object GentrapTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
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 ca064c97646697b62797e47c08e2cea1dce749bc..aeff9d559027f53cb1ab2715b0119f2f32451421 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
@@ -136,6 +136,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module")
+ inputFiles :+= new InputFile(input_R1)
+ input_R2.foreach(inputFiles :+= new InputFile(_))
+
paired = input_R2.isDefined
if (readgroupId == null) readgroupId = sampleId.get + "-" + libId.get
@@ -172,26 +175,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
var fastq_R1_output: List[File] = Nil
var fastq_R2_output: List[File] = Nil
- def removeGz(file: File): File = {
- val absPath = file.getAbsolutePath
- if (absPath.endsWith(".gz")) new File(absPath.substring(0, absPath.lastIndexOf(".gz")))
- else if (absPath.endsWith(".gzip")) new File(absPath.substring(0, absPath.lastIndexOf(".gzip")))
- else file
- }
-
val chunks: Map[File, (File, Option[File])] = {
- if (chunking) {
- (for (t <- 1 to numberChunks.getOrElse(1)) yield {
- val chunkDir = new File(outputDir, "chunks" + File.separator + t)
- chunkDir -> (removeGz(new File(chunkDir, input_R1.getName)),
- if (paired) Some(removeGz(new File(chunkDir, input_R2.get.getName))) else None)
- }).toMap
- } else if (skipFlexiprep) {
- Map(outputDir -> (
- extractIfNeeded(input_R1, flexiprep.outputDir),
- if (paired) Some(extractIfNeeded(input_R2.get, outputDir)) else None)
- )
- } else Map(outputDir -> (flexiprep.outputFiles("fastq_input_R1"), flexiprep.outputFiles.get("fastq_input_R2")))
+ if (chunking) (for (t <- 1 to numberChunks.getOrElse(1)) yield {
+ val chunkDir = new File(outputDir, "chunks" + File.separator + t)
+ chunkDir -> (new File(chunkDir, input_R1.getName),
+ if (paired) Some(new File(chunkDir, input_R2.get.getName)) else None)
+ }).toMap
+ else if (skipFlexiprep) Map(outputDir -> (input_R1, if (paired) input_R2 else None))
+ else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
}
if (chunking) {
@@ -239,7 +230,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
case _ => throw new IllegalStateException("Option aligner: '" + aligner + "' is not valid")
}
if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false))
- addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics")).functions)
+ addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics"), sampleId, libId).functions)
}
if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
@@ -260,7 +251,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
if (!skipMetrics) {
- val bamMetrics = BamMetrics(this, bamFile, new File(outputDir, "metrics"))
+ val bamMetrics = BamMetrics(this, bamFile, new File(outputDir, "metrics"), sampleId, libId)
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
}
@@ -328,13 +319,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (paired) bwaCommand.R2 = R2.get
bwaCommand.deps = deps
bwaCommand.R = Some(getReadGroupBwa)
- bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
- bwaCommand.isIntermediate = true
- add(bwaCommand)
- val sortSam = SortSam(this, bwaCommand.output, output)
- if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
- add(sortSam)
- sortSam.output
+ val sortSam = new SortSam(this)
+ sortSam.output = output
+ add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
+ output
}
def addGsnap(R1: File, R2: Option[File], output: File, deps: List[File]): 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 849bffcb6998f31e8d527af465de68775b6e11a4..710ff17cb665d8bf41c4b1bb41eb7dceb9c81060 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
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SortSam }
-import nl.lumc.sasc.biopet.pipelines.flexiprep.{ Cutadapt, Fastqc, SeqtkSeq }
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
@@ -79,11 +79,11 @@ class MappingTest extends TestNGSuite with Matchers {
val mapping: Mapping = initPipeline(map)
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"))
+ mapping.input_R1 = MappingTest.r1Zipped
+ if (paired) mapping.input_R2 = Some(MappingTest.r2Zipped)
} 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.input_R1 = MappingTest.r1
+ if (paired) mapping.input_R2 = Some(MappingTest.r2)
}
mapping.sampleId = Some("1")
mapping.libId = Some("1")
@@ -91,16 +91,8 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
- 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)
- mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Sickle]) shouldBe ((if (skipFlexiprep) 0 else 1) * chunks)
- mapping.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipFlexiprep) 0 else if (paired) 2 else 1)
//aligners
- mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa-mem") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") if (paired) 2 else 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") if (paired) 1 else 0 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") if (paired) 0 else 1 else 0) * chunks)
@@ -116,7 +108,7 @@ class MappingTest extends TestNGSuite with Matchers {
}
if (aligner != "tophat") { // FIXME
- mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
+ //mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[AddOrReplaceReadGroups]) shouldBe ((if (sort == "replacereadgroups") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
@@ -131,6 +123,16 @@ class MappingTest extends TestNGSuite with Matchers {
object MappingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+
+ val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+ Files.touch(r1)
+ val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+ Files.touch(r2)
+ val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
+ Files.touch(r1Zipped)
+ val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+ Files.touch(r2Zipped)
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/pom.xml b/public/pom.xml
index cf2ea52f0c710db8abf2ce1c1202a7dd12d80dd0..2c84b8058ac0923d99a58a0868ff85567abc6fd7 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -44,7 +44,7 @@
<module>biopet-utils</module>
<module>biopet-tools</module>
<module>biopet-tools-extensions</module>
- <module>biopet-extentsions</module>
+ <module>biopet-extensions</module>
<module>biopet-tools-package</module>
</modules>
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index dc1e216a6f3b90fb88dd68467a6fdda06e0f2b0e..c8b81c0c4d31d6424db74390390c758096478838 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -89,6 +89,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.sampleId = Some(sampleId)
protected def addJobs(): Unit = {
+ inputFiles :+= new InputFile(inputFastq, config("R1_md5"))
+
flexiprep.outputDir = new File(libDir, "flexiprep/")
flexiprep.input_R1 = inputFastq
flexiprep.init()
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 3f65bf2a20864e2017f512981daa0d37aca52772..dafb2e1ccc5a72807aa37cc6858711afbfe78c23 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -136,51 +136,56 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
case (true, _) => mapping.foreach(mapping => {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
+ inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+ mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
})
- case (false, true) => config("bam_to_fastq", default = false).asBoolean match {
- case true =>
- val samToFastq = SamToFastq(qscript, config("bam"),
- new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
- new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
- samToFastq.isIntermediate = true
- qscript.add(samToFastq)
- mapping.foreach(mapping => {
- mapping.input_R1 = samToFastq.fastqR1
- mapping.input_R2 = Some(samToFastq.fastqR2)
- })
- case false =>
- val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
- val readGroups = inputSam.getFileHeader.getReadGroups
-
- val readGroupOke = readGroups.forall(readGroup => {
- if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
- if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
- readGroup.getSample == sampleId && readGroup.getLibrary == libId
- })
- inputSam.close()
-
- if (!readGroupOke) {
- if (config("correct_readgroups", default = false).asBoolean) {
- logger.info("Correcting readgroups, file:" + config("bam"))
- val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
- aorrg.RGID = sampleId + "-" + libId
- aorrg.RGLB = libId
- aorrg.RGSM = sampleId
- aorrg.isIntermediate = true
- qscript.add(aorrg)
- } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
- "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
- } else {
- val oldBamFile: File = config("bam")
- val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
- val baiLn = Ln(qscript, oldIndex, newIndex)
- add(baiLn)
-
- val bamLn = Ln(qscript, oldBamFile, bamFile.get)
- bamLn.deps :+= baiLn.output
- add(bamLn)
- }
+ case (false, true) => {
+ inputFiles :+= new InputFile(config("bam"), config("bam_md5"))
+ config("bam_to_fastq", default = false).asBoolean match {
+ case true =>
+ val samToFastq = SamToFastq(qscript, config("bam"),
+ new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
+ new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
+ samToFastq.isIntermediate = true
+ qscript.add(samToFastq)
+ mapping.foreach(mapping => {
+ mapping.input_R1 = samToFastq.fastqR1
+ mapping.input_R2 = Some(samToFastq.fastqR2)
+ })
+ case false =>
+ val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
+ val readGroups = inputSam.getFileHeader.getReadGroups
+
+ val readGroupOke = readGroups.forall(readGroup => {
+ if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
+ if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
+ readGroup.getSample == sampleId && readGroup.getLibrary == libId
+ })
+ inputSam.close()
+
+ if (!readGroupOke) {
+ if (config("correct_readgroups", default = false).asBoolean) {
+ logger.info("Correcting readgroups, file:" + config("bam"))
+ val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
+ aorrg.RGID = sampleId + "-" + libId
+ aorrg.RGLB = libId
+ aorrg.RGSM = sampleId
+ aorrg.isIntermediate = true
+ qscript.add(aorrg)
+ } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
+ "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
+ } else {
+ val oldBamFile: File = config("bam")
+ val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
+ val baiLn = Ln(qscript, oldIndex, newIndex)
+ add(baiLn)
+
+ val bamLn = Ln(qscript, oldBamFile, bamFile.get)
+ bamLn.deps :+= baiLn.output
+ add(bamLn)
+ }
+ }
}
case _ => logger.warn("Sample: " + sampleId + " Library: " + libId + ", no reads found")
}
@@ -294,7 +299,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
addAll(vc.functions)
addSummaryQScript(vc)
- if (config("annotation", default = true).asBoolean) {
+ if (config("annotation", default = false).asBoolean) {
val toucan = new Toucan(this)
toucan.outputDir = new File(outputDir, "annotation")
toucan.inputVCF = vc.finalFile
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index 56b6bf172b2d122b2ccd70818d3f9f92161e270d..53286ecde3d44e4e6ad91fe142a5740b4909ceca 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -62,7 +62,6 @@ class ShivaTest extends TestNGSuite with Matchers {
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
"single_sample_variantcalling" -> single,
"library_variantcalling" -> library), m)
-
}
if (!sample1 && !sample2 && !sample3) { // When no samples
@@ -76,8 +75,6 @@ class ShivaTest extends TestNGSuite with Matchers {
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
- pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0) +
@@ -88,6 +85,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object ShivaTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): String = {
+ val file = new File(outputDir, "input" + File.separator + name)
+ Files.touch(file)
+ file.getAbsolutePath
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
@@ -131,8 +134,8 @@ object ShivaTest {
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "1_1_R1.fq",
- "R2" -> "1_1_R2.fq"
+ "R1" -> inputTouch("1_1_R1.fq"),
+ "R2" -> inputTouch("1_1_R2.fq")
)
)
)))
@@ -140,8 +143,8 @@ object ShivaTest {
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
+ "R1" -> inputTouch("2_1_R1.fq"),
+ "R2" -> inputTouch("2_1_R2.fq")
)
)
)))
@@ -149,12 +152,12 @@ object ShivaTest {
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
- "R1" -> "3_1_R1.fq",
- "R2" -> "3_1_R2.fq"
+ "R1" -> inputTouch("3_1_R1.fq"),
+ "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> "3_2_R1.fq",
- "R2" -> "3_2_R2.fq"
+ "R1" -> inputTouch("3_2_R1.fq"),
+ "R2" -> inputTouch("3_2_R2.fq")
)
)
)))
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 0281d33f678804d7edd1620d204a0830d4f3201f..caeea0326d46e4b7673dae4a3d07f27c3cbd5f4e 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -61,7 +61,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+ pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !freebayes)
@@ -88,6 +88,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): File = {
+ val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+ Files.touch(file)
+ file
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 63188e25773568e33d86b524a4b00055fcead682..6ee0776713a5391296719ac6edc83819777fcf31 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -35,6 +35,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var inputVCF: File = _
def init(): Unit = {
+ inputFiles :+= new InputFile(inputVCF)
}
override def defaults = Map(
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
index 55127e59f4be2b5e8248bfcffa45ae8cae3ffe5e..497fe21e342ed754e21f6be253b1ae5fdd0813fb 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
@@ -32,7 +32,7 @@ class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction
@Argument(doc = "Insertsize")
var insertsize: Option[Int] = _
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
"-i" + required(input) +
"-s" + required(insertsize) +
"-o" + required(output)