Commit 6c394efd authored by bow's avatar bow
Browse files

Merge branch 'develop' into feature-gentrap

parents 4521305b 46cef440
......@@ -9,6 +9,6 @@ git.properties
# IntelliJ
.idea/*
*.iml
/target/
/public/target/
/protected/target/
target/
public/target/
protected/target/
......@@ -61,7 +61,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
/** return commandline to execute */
def cmdLine = {
required(executable) +
optional("--threads", nCoresRequest) +
optional("--threads", threads) +
conditional(sam, "--sam") +
conditional(best, "--best") +
conditional(strata, "--strata") +
......
......@@ -61,6 +61,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var runmode: String = _
var sjdbOverhang: Int = _
var outFileNamePrefix: String = _
var runThreadN: Option[Int] = config("runThreadN")
override val defaultVmem = "6G"
override val defaultThreads = 8
......@@ -79,6 +80,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
outputSAindex = new File(prefix + "SAindex")
sjdbOverhang = config("sjdboverhang", 75)
}
threads = runThreadN.getOrElse(1)
}
/** Returns command to execute */
......@@ -92,7 +94,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
cmd += required("--genomeDir", genomeDir) +
optional("--sjdbFileChrStartEnd", sjdbFileChrStartEnd) +
optional("--runThreadN", nCoresRequest) +
optional("--runThreadN", threads) +
optional("--outFileNamePrefix", outFileNamePrefix)
if (sjdbOverhang > 0) cmd += optional("--sjdbOverhang", sjdbOverhang)
......
......@@ -51,6 +51,7 @@ class BwaAln(val root: Configurable) extends Bwa {
/** Returns command to execute */
def cmdLine = required(executable) +
required("aln") +
optional("-t", threads) +
optional("-n", n) +
optional("-o", o) +
optional("-e", e) +
......
......@@ -77,7 +77,7 @@ class BwaMem(val root: Configurable) extends Bwa {
required("mem") +
optional("-k", k) +
optional("-r", r) +
optional("-t", nCoresRequest) +
optional("-t", threads) +
optional("-R", R) +
conditional(M, "-M") +
conditional(S, "-S") +
......
......@@ -40,15 +40,26 @@
<module>shiva</module>
<module>basty</module>
</modules>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<scoverage.plugin.version>1.0.4</scoverage.plugin.version>
</properties>
<build>
<sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
<testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
<testResources>
<testResource>
<directory>${basedir}/src/test/resources</directory>
<includes>
<include>**/*</include>
</includes>
</testResource>
</testResources>
<resources>
<resource>
<directory>src/main/resources</directory>
<directory>${basedir}/src/main/resources</directory>
<includes>
<include>**/*</include>
</includes>
......@@ -56,9 +67,9 @@
</resources>
<plugins>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
<version>2.15.2</version>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>scala-compile</id>
......@@ -76,11 +87,19 @@
</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>
......@@ -186,6 +205,27 @@
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
<scalaVersion>2.11.4</scalaVersion>
<!-- other parameters -->
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
<outputDirectory>${basedir}/target/site/scoverage</outputDirectory>
</configuration>
</plugin>
</plugins>
</reporting>
</project>
......@@ -30,7 +30,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript(): Unit = {
val vep = new VariantEffectPredictor(this)
vep.input = inputVCF
vep.output = outputDir + inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf"
vep.output = new File(outputDir, inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf")
vep.isIntermediate = true
add(vep)
......
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