diff --git a/biopet-aggregate/copy-src.sh b/biopet-aggregate/copy-src.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fdfefa48461afe7f1f8e1b4aad226ab818caee25
--- /dev/null
+++ b/biopet-aggregate/copy-src.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+DIR=`readlink -f \`dirname $0\``
+
+cp -r $DIR/../*/*/src/* $DIR/src
+
diff --git a/biopet-aggregate/pom.xml b/biopet-aggregate/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4b89651970b5b9c05bf599a6b14d44b161793663
--- /dev/null
+++ b/biopet-aggregate/pom.xml
@@ -0,0 +1,46 @@
+<?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">
+ <parent>
+ <artifactId>BiopetRoot</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetAggregate</artifactId>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetProtectedPackage</artifactId>
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ <version>18.0</version>
+ </dependency>
+
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/biopet-aggregate/rm-src.sh b/biopet-aggregate/rm-src.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f0a2e2b9307150913a9705bd237f226dc157157e
--- /dev/null
+++ b/biopet-aggregate/rm-src.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+DIR=`readlink -f \`dirname $0\``
+
+rm -r $DIR/src/main $DIR/src/test
+
diff --git a/biopet-aggregate/src/.gitignore b/biopet-aggregate/src/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..59e4d6049a3756e3d0c5414611e042fcc5c1bce6
--- /dev/null
+++ b/biopet-aggregate/src/.gitignore
@@ -0,0 +1,2 @@
+main
+test
diff --git a/pom.xml b/pom.xml
index 143a9095a763bbdcc323dc6e4299e534e5f0bc33..964da3f4aaf87824c6b9fade63d5bc607fe0e0aa 100644
--- a/pom.xml
+++ b/pom.xml
@@ -17,5 +17,6 @@
<module>public</module>
<module>protected</module>
<module>external-example</module>
+ <!--<module>biopet-aggregate</module>-->
</modules>
</project>
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 6b99ca1706a0280a88b881e74e11a644e5ef1ab2..750cbee21adea6c059d939aad518ca9aed0eb06e 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -153,11 +153,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
scriptOutput.rawVcfFile = m2v.output
val vcfFilter = new VcfFilter(this) {
- override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
+ override def defaults = Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
"filter_ref_calls" -> true
- ), super.defaults)
+ )
}
vcfFilter.inputVcf = m2v.output
vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
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 66f0bfcc564503567782bcc1e35b0cc0899e6212..f1b326b7017b129eaf6edf0d44014af4f9507b7b 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
@@ -39,31 +39,27 @@ class ShivaTest extends TestNGSuite with Matchers {
val bool = Array(true, false)
for (
- s1 <- bool; s2 <- bool; s3 <- bool; multi <- bool; single <- bool;
- library <- bool; dbsnp <- bool; covariates <- bool; realign <- bool; baseRecalibration <- bool
- ) yield Array("", s1, s2, s3, multi, single, library, dbsnp, covariates, realign, baseRecalibration)
+ s1 <- bool; s2 <- bool; multi <- bool;
+ dbsnp <- bool; realign <- bool; baseRecalibration <- bool
+ ) yield Array("", s1, s2, multi, dbsnp, realign, baseRecalibration)
}
@Test(dataProvider = "shivaOptions")
- def testShiva(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean,
- multi: Boolean, single: Boolean, library: Boolean, dbsnp: Boolean,
- covariates: Boolean, realign: Boolean, baseRecalibration: Boolean): Unit = {
+ def testShiva(f: String, sample1: Boolean, sample2: Boolean,
+ multi: Boolean, dbsnp: Boolean,
+ realign: Boolean, baseRecalibration: Boolean): Unit = {
val map = {
var m: Map[String, Any] = ShivaTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m)
if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m)
- if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test"), m)
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
- "single_sample_variantcalling" -> single,
- "library_variantcalling" -> library,
- "use_analyze_covariates" -> covariates,
"use_indel_realigner" -> realign,
"use_base_recalibration" -> baseRecalibration), m)
}
- if (!sample1 && !sample2 && !sample3) { // When no samples
+ if (!sample1 && !sample2) { // When no samples
intercept[IllegalArgumentException] {
initPipeline(map).script()
}
@@ -71,20 +67,18 @@ class ShivaTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(map)
pipeline.script()
- 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)
+ val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
+ val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))
// Gatk preprocess
- pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs + (if (sample3) 1 else 0)) * (if (realign) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs + (if (sample3) 1 else 0)) * (if (realign) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0) * (if (covariates) 2 else 1)
- pipeline.functions.count(_.isInstanceOf[AnalyzeCovariates]) shouldBe (if (dbsnp && covariates && baseRecalibration) numberLibs else 0)
+ pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
- pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0) +
- (if (single) numberSamples * 2 else 0) + (if (library) numberLibs * 2 else 0)
+ pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0)
}
}
}
@@ -115,7 +109,6 @@ object ShivaTest {
"dir" -> "test",
"vep_script" -> "test",
"output_dir" -> outputDir,
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
@@ -147,23 +140,14 @@ object ShivaTest {
)))
val sample2 = Map(
- "samples" -> Map("sample2" -> Map("libraries" -> Map(
+ "samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> inputTouch("2_1_R1.fq"),
"R2" -> inputTouch("2_1_R2.fq")
- )
- )
- )))
-
- val sample3 = Map(
- "samples" -> Map("sample3" -> Map("libraries" -> Map(
- "lib1" -> Map(
- "R1" -> inputTouch("3_1_R1.fq"),
- "R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
- "R1" -> inputTouch("3_2_R1.fq"),
- "R2" -> inputTouch("3_2_R2.fq")
+ "R1" -> inputTouch("2_2_R1.fq"),
+ "R2" -> inputTouch("2_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 8e8a1eddf9e5d6b5aab36c4c6fea7d35ea2da82e..1740b33ac108a4c20205973a2410aabbeb4dbd83 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
@@ -131,7 +131,6 @@ object ShivaVariantcallingTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
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 ab6692982d698ef8d4ea41593f07b55b01671db8..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
@@ -35,10 +35,10 @@ trait BastyTrait extends MultiSampleQScript {
def variantcallers = List("freebayes")
- override def defaults = ConfigUtils.mergeMaps(Map(
+ override def defaults = Map(
"ploidy" -> 1,
"variantcallers" -> variantcallers
- ), super.defaults)
+ )
lazy val shiva: ShivaTrait = new Shiva(qscript)
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
index 300cd4cdb0d240f19c709ac53e35b180e8675504..0fdc946e31808db3b41eb7e81bd5377c3ec563f3 100644
--- 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
@@ -85,9 +85,11 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
this.freeze()
}
+ var threadsCorrection = 0
+
protected def combineResources(commands: List[CommandLineResources]): Unit = {
commands.foreach(_.setResources())
- nCoresRequest = Some(commands.map(_.threads).sum)
+ nCoresRequest = Some(commands.map(_.threads).sum + threadsCorrection)
_coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
memoryLimit = Some(_coreMemory * threads)
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 98%
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
index 5a574b729fb7fa4c7b27c674845f069fd01cb4ca..fc2f95e4e33f54dca689568bb48cb8489ed3e65d 100644
--- 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
@@ -47,7 +47,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
override def defaultCoreMemory = 4.0
override def defaultThreads = 8
- var sam: Boolean = config("sam", default = true)
+ var sam: Boolean = config("sam", default = false)
var sam_RG: Option[String] = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var seedmms: Option[Int] = config("seedmms")
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 97%
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 5c7ebd0ca6382584bc45b455527e50bdede1a673..be5eb6700c6c1610c33c0e1f0fa132089db81bfc 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
@@ -36,7 +36,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
/** Returns command to execute */
def cmdLine = required(executable) +
- (if (inputAsStdin) "" else required(input)) +
+ (if (inputAsStdin) "" else repeat(input)) +
(if (outputAsStsout) "" else " > " + required(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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
new file mode 100644
index 0000000000000000000000000000000000000000..392169043c9fa8e10852b4ff61694892c7531b3c
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by sajvanderzeeuw on 6-10-15.
+ */
+class BuildBamIndex(val root: Configurable) extends Picard {
+
+ javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
+
+ @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+ var input: File = _
+
+ @Output(doc = "The output file to bam file to", required = true)
+ var output: File = _
+
+ override def cmdLine = super.cmdLine +
+ 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 100%
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
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 93%
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 ff19efe11676d2ca66adc172790080f9a9823783..b2fb2097efefb107ab4f00c3cadde5e9285a2568 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
@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
+import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard CollectAlignmentSummaryMetrics */
-class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
@@ -41,7 +42,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
var output: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference")
+ var reference: File = _
@Argument(doc = "ASSUME_SORTED", required = false)
var assumeSorted: Boolean = config("assumeSorted", default = true)
@@ -52,6 +53,11 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
@Argument(doc = "STOP_AFTER", required = false)
var stopAfter: Option[Long] = config("stopAfter")
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ if (reference == null) reference = referenceFasta()
+ }
+
/** Returns command to execute */
override def cmdLine = super.cmdLine +
required("INPUT=", input, 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 ada8007283b76122005cc5d4e6a0a39c161ea1aa..0479bbb754d62a13e4e7d99bf6ac949b8cd69aec 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
@@ -53,6 +53,8 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
@Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
+ override def defaultCoreMemory = 8.0
+
override def beforeGraph() {
super.beforeGraph()
if (outputChart == null) outputChart = new File(output + ".pdf")
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 95%
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 3c4693b5ead3929b9b1bf7eac95b69c3bed0c83c..88d2eab6091ef4dafa02b46395ac1c78188ee3c2 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
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
+import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
@@ -24,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.collection.immutable.Nil
/** Extension for picard CollectInsertSizeMetrics */
-class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
javaMainClass = new picard.analysis.CollectInsertSizeMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
@@ -37,7 +38,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
protected var outputHistogram: File = null
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference")
+ var reference: File = _
@Argument(doc = "DEVIATIONS", required = false)
var deviations: Option[Double] = config("deviations")
@@ -59,6 +60,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
override def beforeGraph() {
outputHistogram = new File(output + ".pdf")
+ if (reference == null) reference = referenceFasta()
}
/** Returns command to execute */
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 99%
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 5ddaa72341c6a35b6cc9070c6d50cc48e80b7551..fed464a7391ad3f618e3755c2b8addc3cfb608b1 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
@@ -33,7 +33,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
javaMainClass = new picard.analysis.CollectMultipleMetrics().getClass.getName
- override def defaultCoreMemory = 6.0
+ override def defaultCoreMemory = 8.0
@Input(doc = "The input SAM or BAM files to analyze", required = true)
var input: File = null
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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
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-extentsions/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
similarity index 91%
rename from public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
index 4d1c7450e5ac3fbf7c670305c49b6b188d11c6bc..5df2a3a7b47f5771dcdbd033ef2c273ba70ed89f 100644
--- a/public/biopet-extentsions/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
@@ -2,9 +2,8 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
-import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 22/09/15.
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 96%
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
index fca6e84ccd15bfd6af4c72723269e13afda7f13c..09e8bff4212602d0689ea4f43eeee947b29c870e 100644
--- 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
@@ -28,7 +28,7 @@ class SamtoolsView(val root: Configurable) extends Samtools {
@Output(doc = "output File")
var output: File = null
- var quality: Option[Int] = config("quality")
+ var q: Option[Int] = config("q")
var b: Boolean = config("b", default = false)
var h: Boolean = config("h", default = false)
var f: List[String] = config("f", default = List.empty[String])
@@ -36,7 +36,7 @@ class SamtoolsView(val root: Configurable) extends Samtools {
def cmdBase = required(executable) +
required("view") +
- optional("-q", quality) +
+ optional("-q", q) +
repeat("-f", f) +
repeat("-F", F) +
conditional(b, "-b") +
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 100%
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
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 100%
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
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 77%
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
index 7a5a541899981f9a3a6bf25396ea23d64afd60d3..8dceeb52502cf5b150bc3fa4e41ccdb9cb6aebae 100644
--- 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
@@ -25,17 +25,10 @@ import scala.sys.process.{ Process, ProcessLogger }
class GsnapTest extends TestNGSuite with Matchers {
- private def setConfig(key: String, value: String): Map[String, Any] = {
- val oldMap: Map[String, Any] = Config.global.map
- Config.global.map += (key -> value)
- oldMap
- }
-
- private def restoreConfig(oldMap: Map[String, Any]): Unit = Config.global.map = oldMap
-
@BeforeClass def checkExecutable() = {
- val oldMap = setConfig("db", "mock")
- val wrapper = new Gsnap(null)
+ val wrapper = new Gsnap(null) {
+ override def globalConfig = new Config(Map("db" -> "mock"))
+ }
val proc = Process(wrapper.versionCommand)
val exitCode =
try {
@@ -47,13 +40,12 @@ class GsnapTest extends TestNGSuite with Matchers {
}
if (exitCode != 0)
throw new SkipException("Skipping GSNAP test because the executable can not be found")
- restoreConfig(oldMap)
}
@Test(description = "GSNAP version number capture from executable")
def testVersion() = {
- val oldMap = setConfig("db", "mock")
- new Gsnap(null).getVersion should not be "N/A"
- restoreConfig(oldMap)
+ new Gsnap(null) {
+ override def globalConfig = new Config(Map("db" -> "mock"))
+ }.getVersion should not be "N/A"
}
}
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-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
index 1d536084f976312300c091744a99a01a4ae4c3e3..4c69bf57c8be5332aeb3f1cc3d1f78b2ae204007 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
@@ -21,11 +21,11 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils._
/**
* This class can store nested config values
- * @param map Map with value for new config
+ * @param _map Map with value for new config
* @constructor Load config with existing map
*/
-class Config(var map: Map[String, Any],
- protected[config] var defaults: Map[String, Any] = Map()) extends Logging {
+class Config(protected var _map: Map[String, Any],
+ protected var _defaults: Map[String, Any] = Map()) extends Logging {
logger.debug("Init phase of config")
/** Default constructor */
@@ -34,6 +34,9 @@ class Config(var map: Map[String, Any],
loadDefaultConfig()
}
+ def map = _map
+ def defaults = _defaults
+
/**
* Loading a environmental variable as location of config files to merge into the config
* @param valueName Name of value
@@ -65,13 +68,13 @@ class Config(var map: Map[String, Any],
def loadConfigFile(configFile: File, default: Boolean = false) {
val configMap = fileToConfigMap(configFile)
if (default) {
- if (defaults.isEmpty) defaults = configMap
- else defaults = mergeMaps(configMap, defaults)
- logger.debug("New defaults: " + defaults)
+ if (_defaults.isEmpty) _defaults = configMap
+ else _defaults = mergeMaps(configMap, _defaults)
+ logger.debug("New defaults: " + _defaults)
} else {
- if (map.isEmpty) map = configMap
- else map = mergeMaps(configMap, map)
- logger.debug("New config: " + map)
+ if (_map.isEmpty) _map = configMap
+ else _map = mergeMaps(configMap, _map)
+ logger.debug("New config: " + _map)
}
}
@@ -84,11 +87,12 @@ class Config(var map: Map[String, Any],
*/
def addValue(key: String, value: Any, path: List[String] = Nil, default: Boolean = false): Unit = {
val valueMap = path.foldRight(Map(key -> value))((a, b) => Map(a -> b))
- if (default) defaults = mergeMaps(valueMap, defaults)
- else map = mergeMaps(valueMap, map)
+ if (default) _defaults = mergeMaps(valueMap, _defaults)
+ else _map = mergeMaps(valueMap, _map)
}
protected[config] var notFoundCache: List[ConfigValueIndex] = List()
+ protected[config] var fixedCache: Map[ConfigValueIndex, ConfigValue] = Map()
protected[config] var foundCache: Map[ConfigValueIndex, ConfigValue] = Map()
protected[config] var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()
protected[config] def clearCache(): Unit = {
@@ -103,24 +107,39 @@ class Config(var map: Map[String, Any],
* @param s key
* @return True if exist
*/
- def contains(s: String): Boolean = map.contains(s)
+ def contains(s: String): Boolean = _map.contains(s)
+
+ /**
+ * Checks if value exist in config
+ * @param requestedIndex Index to value
+ * @return True if exist
+ */
+ def contains(requestedIndex: ConfigValueIndex): Boolean = contains(requestedIndex, Map())
/**
* Checks if value exist in config
* @param requestedIndex Index to value
+ * @param fixedValues Fixed values
* @return True if exist
*/
- def contains(requestedIndex: ConfigValueIndex): Boolean =
+ def contains(requestedIndex: ConfigValueIndex, fixedValues: Map[String, Any]): Boolean =
if (notFoundCache.contains(requestedIndex)) false
+ else if (fixedCache.contains(requestedIndex)) true
else if (foundCache.contains(requestedIndex)) true
else {
- val value = Config.getValueFromMap(map, requestedIndex)
- if (value.isDefined && value.get.value != None) {
- foundCache += (requestedIndex -> value.get)
+ val fixedValue = Config.getValueFromMap(fixedValues, requestedIndex)
+ if (fixedValue.isDefined) {
+ fixedCache += (requestedIndex -> fixedValue.get)
true
} else {
- notFoundCache +:= requestedIndex
- false
+ val value = Config.getValueFromMap(_map, requestedIndex)
+ if (value.isDefined && value.get.value != None) {
+ foundCache += (requestedIndex -> value.get)
+ true
+ } else {
+ notFoundCache +:= requestedIndex
+ false
+ }
}
}
@@ -132,9 +151,12 @@ class Config(var map: Map[String, Any],
* @param freeVar Default true, if set false value must exist in module
* @return True if exist
*/
- def contains(module: String, path: List[String], key: String, freeVar: Boolean = true): Boolean = {
+ def contains(module: String, path: List[String],
+ key: String,
+ freeVar: Boolean = true,
+ fixedValues: Map[String, Any] = Map()): Boolean = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- contains(requestedIndex)
+ contains(requestedIndex, fixedValues)
}
/**
@@ -146,10 +168,23 @@ class Config(var map: Map[String, Any],
* @param freeVar Default true, if set false value must exist in module
* @return Config value
*/
- protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
+ protected[config] def apply(module: String,
+ path: List[String],
+ key: String,
+ default: Any = null,
+ freeVar: Boolean = true,
+ fixedValues: Map[String, Any] = Map()): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- if (contains(requestedIndex)) foundCache(requestedIndex)
- else if (default != null) {
+ if (contains(requestedIndex, fixedValues)) {
+ val fixedValue = fixedCache.get(requestedIndex)
+ if (fixedValue.isDefined) {
+ val userValue = Config.getValueFromMap(_map, requestedIndex)
+ if (userValue.isDefined)
+ logger.warn(s"Ignoring user-supplied value ${requestedIndex.key} at path ${requestedIndex.path} because it is a fixed value.")
+ }
+
+ fixedValue.getOrElse(foundCache(requestedIndex))
+ } else if (default != null) {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
defaultCache(requestedIndex)
} else ConfigValue(requestedIndex, null, null, freeVar)
@@ -179,9 +214,11 @@ class Config(var map: Map[String, Any],
// Positions where values are found
val found = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
+ val fixed = convertIndexValuesToMap(fixedCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
// Positions where to start searching
val effectiveFound = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
+ val effectiveFixed = convertIndexValuesToMap(fixedCache.filter(!_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
val effectiveDefaultFound = convertIndexValuesToMap(defaultCache.filter(_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
val notFound = convertIndexValuesToMap(notFoundCache.map((_, None)), Some(false))
@@ -189,16 +226,19 @@ class Config(var map: Map[String, Any],
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(this.map, "input")
+ writeMapToJsonFile(_map, "input")
+ writeMapToJsonFile(_defaults, "defaults")
writeMapToJsonFile(found, "found")
+ writeMapToJsonFile(fixed, "fixed")
writeMapToJsonFile(effectiveFound, "effective.found")
+ writeMapToJsonFile(effectiveFixed, "effective.fixed")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
writeMapToJsonFile(notFound, "not.found")
writeMapToJsonFile(fullEffective, "effective.full")
writeMapToJsonFile(fullEffectiveWithNotFound, "effective.full.notfound")
}
- override def toString: String = map.toString()
+ override def toString: String = _map.toString()
}
object Config extends Logging {
@@ -210,7 +250,7 @@ object Config extends Logging {
* @param config2 Low prio map
* @return Merged config
*/
- def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1.map, config2.map))
+ def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1._map, config2._map))
/**
* Search for value in index position in a map
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
index 476c4c4435290a9229bc926695cb9153d996d75a..68fe36e303e6a49e96a7628a741fc120392a5d19 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
@@ -15,6 +15,7 @@
*/
package nl.lumc.sasc.biopet.utils.config
+import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
trait Configurable extends ImplicitConversions {
@@ -35,9 +36,28 @@ trait Configurable extends ImplicitConversions {
def configFullPath: List[String] = configPath ::: configName :: Nil
/** Map to store defaults for config */
- def defaults: Map[String, Any] = {
- if (root != null) root.defaults
- else globalConfig.defaults
+ def defaults: Map[String, Any] = Map()
+
+ /** This method merge defaults from the root to it's own */
+ protected[config] def internalDefaults: Map[String, Any] = {
+ (root != null, defaults.isEmpty) match {
+ case (true, true) => root.internalDefaults
+ case (true, false) => ConfigUtils.mergeMaps(defaults, root.internalDefaults)
+ case (false, true) => globalConfig.defaults
+ case (false, false) => ConfigUtils.mergeMaps(defaults, globalConfig.defaults)
+ }
+ }
+
+ /** All values found in this map will be skipped from the user config */
+ def fixedValues: Map[String, Any] = Map()
+
+ /** This method merge fixedValues from the root to it's own */
+ protected def internalFixedValues: Map[String, Any] = {
+ (root != null, fixedValues.isEmpty) match {
+ case (true, true) => root.internalFixedValues
+ case (true, false) => ConfigUtils.mergeMaps(fixedValues, root.internalFixedValues)
+ case _ => fixedValues
+ }
}
val config = new ConfigFunctions
@@ -90,11 +110,11 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
val d = {
- val value = Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar))
+ val value = Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (d == null) globalConfig(m, p, key, freeVar = freeVar)
- else globalConfig(m, p, key, d, freeVar)
+ if (d == null) globalConfig(m, p, key, freeVar = freeVar, fixedValues = internalFixedValues)
+ else globalConfig(m, p, key, d, freeVar, fixedValues = internalFixedValues)
}
/**
@@ -117,7 +137,7 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
- globalConfig.contains(m, p, key, freeVar) || Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
+ globalConfig.contains(m, p, key, freeVar, internalFixedValues) || Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
}
}
}
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
index 8853a1183870f304c3529c43c569365c33437a27..37e851cf1572848a648bcb45ff5b7a51edeb0a68 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
@@ -25,10 +25,36 @@ import org.testng.annotations.Test
* Created by pjvan_thof on 1/8/15.
*/
class ConfigurableTest extends TestNGSuite with Matchers {
+
+ abstract class Cfg extends Configurable {
+ def get(key: String,
+ default: String = null,
+ submodule: String = null,
+ freeVar: Boolean = true,
+ sample: String = null,
+ library: String = null) = {
+ config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
+ }
+ }
+
+ class ClassA(val root: Configurable) extends Cfg
+
+ class ClassB(val root: Configurable) extends Cfg {
+ lazy val classA = new ClassA(this)
+ // Why this needs to be lazy?
+ }
+
+ class ClassC(val root: Configurable) extends Cfg {
+ def this() = this(null)
+ lazy val classB = new ClassB(this)
+ // Why this needs to be lazy?
+ }
+
@Test def testConfigurable(): Unit = {
val classC = new ClassC {
override def configName = "classc"
override val globalConfig = new Config(ConfigurableTest.map)
+ override val fixedValues = Map("fixed" -> "fixed")
}
classC.configPath shouldBe Nil
@@ -51,46 +77,33 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC.get("bla", sample = "sample1", library = "library1").asString shouldBe "bla"
classC.get("test", sample = "sample1", library = "library1").asString shouldBe "test"
classC.get("test", sample = "sample1").asString shouldBe "test"
- }
-}
-abstract class Cfg extends Configurable {
- def get(key: String,
- default: String = null,
- submodule: String = null,
- freeVar: Boolean = true,
- sample: String = null,
- library: String = null) = {
- config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
+ // Fixed values
+ classC.get("fixed").asString shouldBe "fixed"
+ classC.classB.get("fixed").asString shouldBe "fixed"
+ classC.classB.classA.get("fixed").asString shouldBe "fixed"
}
}
-class ClassA(val root: Configurable) extends Cfg
-
-class ClassB(val root: Configurable) extends Cfg {
- lazy val classA = new ClassA(this)
- // Why this needs to be lazy?
-}
-
-class ClassC(val root: Configurable) extends Cfg {
- def this() = this(null)
- lazy val classB = new ClassB(this)
- // Why this needs to be lazy?
-}
-
object ConfigurableTest {
val map = Map(
+ "fixed" -> "nonfixed",
"classa" -> Map(
- "k1" -> "a1"
+ "k1" -> "a1",
+ "fixed" -> "nonfixed"
), "classb" -> Map(
- "k1" -> "b1"
+ "k1" -> "b1",
+ "fixed" -> "nonfixed"
), "classc" -> Map(
- "k1" -> "c1"
+ "k1" -> "c1",
+ "fixed" -> "nonfixed"
), "samples" -> Map(
"sample1" -> Map(
+ "fixed" -> "nonfixed",
"test" -> "test",
"libraries" -> Map(
"library1" -> Map(
+ "fixed" -> "nonfixed",
"bla" -> "bla"
)
)
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 f8b4dc6db0ff771d046ffe320a24a7c0d294b832..de37b352ecf8a9091ee67d1b455e85087156f642 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
@@ -18,11 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
-import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+import nl.lumc.sasc.biopet.extensions.picard.{ BuildBamIndex, MergeSamFiles }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
@@ -38,12 +39,20 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
qscript =>
def this() = this(null)
- override def defaults = ConfigUtils.mergeMaps(Map(
+ override def defaults = Map(
"mapping" -> Map(
- "skip_markduplicates" -> true,
+ "skip_markduplicates" -> false,
"aligner" -> "bwa-mem"
+ ),
+ "samtoolsview" -> Map("q" -> 10)
+ )
+
+ override def fixedValues = Map(
+ "samtoolsview" -> Map(
+ "h" -> true,
+ "b" -> true
)
- ), super.defaults)
+ )
def summaryFile = new File(outputDir, "Carp.summary.json")
@@ -93,6 +102,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
}
val bamFile = createFile(".bam")
+ val bamFileFilter = createFile(".filter.bam")
val controls: List[String] = config("control", default = Nil)
def addJobs(): Unit = {
@@ -114,10 +124,29 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
+
+ val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
+ addAll(bamMetricsFilter.functions)
+ bamMetricsFilter.summaryName = "bammetrics-filter"
+ addSummaryQScript(bamMetricsFilter)
+
addAll(Bam2Wig(qscript, bamFile).functions)
+ addAll(Bam2Wig(qscript, bamFileFilter).functions)
+
+ val samtoolsView = new SamtoolsView(qscript)
+ samtoolsView.input = bamFile
+ samtoolsView.output = bamFileFilter
+ samtoolsView.b = true
+ samtoolsView.h = true
+ add(samtoolsView)
+
+ val buildBamIndex = new BuildBamIndex(qscript)
+ buildBamIndex.input = bamFileFilter
+ buildBamIndex.output = swapExt(bamFileFilter.getParent, bamFileFilter, ".bam", ".bai")
+ add(buildBamIndex)
val macs2 = new Macs2CallPeak(qscript)
- macs2.treatment = bamFile
+ macs2.treatment = bamFileFilter
macs2.name = Some(sampleId)
macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
add(macs2)
@@ -155,8 +184,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
if (!samples.contains(controlId))
throw new IllegalStateException("For sample: " + sampleId + " this control: " + controlId + " does not exist")
val macs2 = new Macs2CallPeak(this)
- macs2.treatment = sample.bamFile
- macs2.control = samples(controlId).bamFile
+ macs2.treatment = sample.bamFileFilter
+ macs2.control = samples(controlId).bamFileFilter
macs2.name = Some(sampleId + "_VS_" + controlId)
macs2.outputdir = sample.sampleDir + File.separator + "macs2" + File.separator + macs2.name.get + File.separator
add(macs2)
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 1f5efdc2fb950dfca40e7a870bba7da984db0c41..da5d79939fd3729fb8838ab26bbe1a2d2d2bfb00 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
@@ -116,7 +116,6 @@ object CarpTest {
copyFile("ref.fa.fai")
val executables = Map(
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
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 6c444bed885b3b4219728bf38423156b3d545064..8de84c5081db4b9801222c6853e2b185a54741e6 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
@@ -201,7 +201,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
def summaryStats: Map[String, Any] = Map(
"per_base_sequence_quality" -> perBaseSequenceQuality,
- "per_base_sequence_content" -> perBaseSequenceContent)
+ "per_base_sequence_content" -> perBaseSequenceContent,
+ "adapters" -> foundAdapters.map(x => x.name -> x.seq).toMap)
}
object Fastqc {
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 aeab29b7d697093726674b263f916faf77bccd7d..e53c55cc53bd4cddab07de2d1fe7a1f5bc25feb9 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
@@ -153,29 +153,31 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
else None
/** Adds all chunkable jobs of flexiprep */
- def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, Option[File], List[File]) =
+ def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, Option[File]) =
runTrimClip(R1_in, None, outDir, chunk)
/** Adds all chunkable jobs of flexiprep */
- def runTrimClip(R1_in: File, outDir: File): (File, Option[File], List[File]) =
+ def runTrimClip(R1_in: File, outDir: File): (File, Option[File]) =
runTrimClip(R1_in, None, outDir, "")
/** Adds all chunkable jobs of flexiprep */
- def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File): (File, Option[File], List[File]) =
+ def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File): (File, Option[File]) =
runTrimClip(R1_in, R2_in, outDir, "")
/** Adds all chunkable jobs of flexiprep */
- def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File, chunkarg: String): (File, Option[File], List[File]) = {
+ def runTrimClip(R1_in: File,
+ R2_in: Option[File],
+ outDir: File,
+ chunkarg: String): (File, Option[File]) = {
val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_"
var R1 = R1_in
var R2 = R2_in
- def deps: List[File] = Nil
val qcCmdR1 = new QcCommand(this, fastqc_R1)
qcCmdR1.input = R1_in
qcCmdR1.read = "R1"
- qcCmdR1.output = if (paired) new File(fastqR1Qc.getAbsolutePath.stripSuffix(".gz"))
+ qcCmdR1.output = if (paired) new File(outDir, fastqR1Qc.getName.stripSuffix(".gz"))
else fastqR1Qc
qcCmdR1.deps :+= fastqc_R1.output
qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
@@ -184,7 +186,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (paired) {
val qcCmdR2 = new QcCommand(this, fastqc_R2)
qcCmdR2.input = R2_in.get
- qcCmdR2.output = new File(fastqR2Qc.get.getAbsolutePath.stripSuffix(".gz"))
+ qcCmdR2.output = new File(outDir, fastqR2Qc.get.getName.stripSuffix(".gz"))
qcCmdR2.read = "R2"
addSummarizable(qcCmdR2, "qc_command_R2")
@@ -195,8 +197,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.refFastq = R1_in
fqSync.inputFastq1 = qcCmdR1.output
fqSync.inputFastq2 = qcCmdR2.output
- fqSync.outputFastq1 = fastqR1Qc
- fqSync.outputFastq2 = fastqR2Qc.get
+ fqSync.outputFastq1 = new File(outDir, fastqR1Qc.getName)
+ fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
val pipe = new BiopetFifoPipe(this, fqSync :: Nil) {
@@ -242,7 +244,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += (chunk + "output_R1" -> R1)
if (paired) outputFiles += (chunk + "output_R2" -> R2.get)
- (R1, R2, deps)
+ (R1, R2)
}
/** Adds last non chunkable jobs */
@@ -250,24 +252,28 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (fastq_R1.length != fastq_R2.length && paired)
throw new IllegalStateException("R1 and R2 file number is not the same")
- if (!skipTrim || !skipClip) {
- 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)
+ if (fastq_R1.length > 1) {
+ val zcat = new Zcat(this)
+ zcat.input = fastq_R1
+ add(zcat | new Gzip(this) > fastqR1Qc)
+ if (paired) {
+ val zcat = new Zcat(this)
+ zcat.input = fastq_R2
+ add(zcat | new Gzip(this) > fastqR2Qc.get)
}
+ }
- outputFiles += ("output_R1_gzip" -> fastqR1Qc)
- if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
+ outputFiles += ("output_R1_gzip" -> fastqR1Qc)
+ if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
- fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
- add(fastqc_R1_after)
- addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
+ 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, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
- add(fastqc_R2_after)
- addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
- }
+ if (paired) {
+ 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")
}
addSummaryJobs()
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 f7f9dc2ab2d916e22c0a6858663f1a43773f7f22..cce952717b29e94556d3535cab4c5830d33a1cfe 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
@@ -73,11 +73,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
flexiprep.libId = Some("1")
flexiprep.script()
- flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (
- if (paired && (skipClip && skipTrim)) 2
- else if (!paired && (skipClip && skipTrim)) 1
- else if (paired && !(skipClip && skipTrim)) 4
- else if (!paired && !(skipClip && skipTrim)) 2)
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (paired) 4 else 2)
flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
}
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 d033594c6e42663427108baf12038b7eed6fb3f6..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
@@ -100,24 +100,23 @@ class Gentrap(val root: Configurable) extends QScript
})
/** Default pipeline config */
- override def defaults = ConfigUtils.mergeMaps(
- Map(
- "gsnap" -> Map(
- "novelsplicing" -> 1,
- "batch" -> 4,
- "format" -> "sam"
- ),
- "cutadapt" -> Map("minimum_length" -> 20),
- // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
- "picard" -> Map(
- "programrecordid" -> "null"
- ),
- // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
- "mapping" -> Map(
- "skip_markduplicates" -> true,
- "skip_metrics" -> true
- )
- ), super.defaults)
+ override def defaults = Map(
+ "gsnap" -> Map(
+ "novelsplicing" -> 1,
+ "batch" -> 4,
+ "format" -> "sam"
+ ),
+ "cutadapt" -> Map("minimum_length" -> 20),
+ // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
+ "picard" -> Map(
+ "programrecordid" -> "null"
+ ),
+ // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
+ "mapping" -> Map(
+ "skip_markduplicates" -> true,
+ "skip_metrics" -> true
+ )
+ )
/** Adds output merge jobs for the given expression mode */
// TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)
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 2b2ddaf259e8fa5ad382ef1aca1337826ecf0ad8..34a43484056b82d9948a11c16f7c2276be7bd6e8 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
@@ -28,7 +28,7 @@ import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ AfterClass, DataProvider, Test }
-class GentrapTest extends TestNGSuite with Matchers {
+abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Gentrap = {
new Gentrap() {
@@ -70,7 +70,7 @@ class GentrapTest extends TestNGSuite with Matchers {
.toMap
)
- private lazy val validExpressionMeasures = Set(
+ val validExpressionMeasures = Set(
"fragments_per_gene", "fragments_per_exon", "bases_per_gene", "bases_per_exon",
"cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
@@ -96,7 +96,7 @@ class GentrapTest extends TestNGSuite with Matchers {
for {
sampleConfig <- sampleConfigs.toArray
- expressionMeasure <- expressionMeasures
+ //expressionMeasure <- expressionMeasures
strandProtocol <- strandProtocols
} yield Array(sampleConfig, List(expressionMeasure), strandProtocol)
}
@@ -118,8 +118,6 @@ class GentrapTest extends TestNGSuite with Matchers {
val functions = gentrap.functions.groupBy(_.getClass)
val numSamples = sampleConfig("samples").size
- functions(classOf[Gsnap]).size should be >= 1
-
if (expMeasures.contains("fragments_per_gene")) {
gentrap.functions
.collect { case x: HtseqCount => x.output.toString.endsWith(".fragments_per_gene") }.size shouldBe numSamples
@@ -177,6 +175,14 @@ class GentrapTest extends TestNGSuite with Matchers {
}
}
+class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene")
+class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon")
+class GentrapBasesPerGeneTest extends GentrapTestAbstract("bases_per_gene")
+class GentrapBasesPerExonTest extends GentrapTestAbstract("bases_per_exon")
+class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict")
+class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided")
+class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind")
+
object GentrapTest {
val outputDir = Files.createTempDir()
new File(outputDir, "input").mkdirs()
@@ -198,7 +204,6 @@ object GentrapTest {
copyFile("ref.fa.fai")
val executables = Map(
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"refFlat" -> "test",
"annotation_gtf" -> "test",
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 d0a78797c8b14ddbfbad3b1b6de7947280032cfc..eb52e5ab931c516333c4582f3373787d9922408e 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
@@ -98,13 +98,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** location of summary file */
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
- override def defaults = ConfigUtils.mergeMaps(
- Map(
- "gsnap" -> Map(
- "batch" -> 4,
- "format" -> "sam"
- )
- ), super.defaults)
+ override def defaults = Map("gsnap" -> Map("batch" -> 4))
+
+ override def fixedValues = Map(
+ "gsnap" -> Map("format" -> "sam"),
+ "bowtie" -> Map("sam" -> true)
+ )
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
@@ -118,7 +117,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"skip_markduplicates" -> skipMarkduplicates,
"aligner" -> aligner,
"chunking" -> chunking,
- "numberChunks" -> numberChunks.getOrElse(1)
+ "numberChunks" -> (if (chunking) numberChunks.getOrElse(1) else None)
) ++ (if (root == null) Map("reference" -> referenceSummary) else Map())
override def reportClass = {
@@ -143,8 +142,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
paired = input_R2.isDefined
- if (readgroupId == null) readgroupId = sampleId.get + "-" + libId.get
- else if (readgroupId == null) readgroupId = config("readgroup_id")
+ if (readgroupId == null)
+ readgroupId = config("readgroup_id", default = sampleId.get + "-" + libId.get)
if (outputName == null) outputName = readgroupId
@@ -206,13 +205,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
for ((chunkDir, fastqfile) <- chunks) {
var R1 = fastqfile._1
var R2 = fastqfile._2
- var deps: List[File] = Nil
if (!skipFlexiprep) {
val flexiout = flexiprep.runTrimClip(R1, R2, new File(chunkDir, "flexiprep"), chunkDir)
logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
- deps = flexiout._3
fastq_R1_output :+= R1
R2.foreach(R2 => fastq_R2_output :+= R2)
}
@@ -220,15 +217,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val outputBam = new File(chunkDir, outputName + ".bam")
bamFiles :+= outputBam
aligner match {
- case "bwa-mem" => addBwaMem(R1, R2, outputBam, deps)
- case "bwa-aln" => addBwaAln(R1, R2, outputBam, deps)
- case "bowtie" => addBowtie(R1, R2, outputBam, deps)
- case "gsnap" => addGsnap(R1, R2, outputBam, deps)
+ case "bwa-mem" => addBwaMem(R1, R2, outputBam)
+ case "bwa-aln" => addBwaAln(R1, R2, outputBam)
+ case "bowtie" => addBowtie(R1, R2, outputBam)
+ case "gsnap" => addGsnap(R1, R2, outputBam)
// TODO: make TopHat here accept multiple input files
- case "tophat" => addTophat(R1, R2, outputBam, deps)
- case "stampy" => addStampy(R1, R2, outputBam, deps)
- case "star" => addStar(R1, R2, outputBam, deps)
- case "star-2pass" => addStar2pass(R1, R2, outputBam, deps)
+ case "tophat" => addTophat(R1, R2, outputBam)
+ case "stampy" => addStampy(R1, R2, outputBam)
+ case "star" => addStar(R1, R2, outputBam)
+ case "star-2pass" => addStar2pass(R1, R2, outputBam)
case _ => throw new IllegalStateException("Option aligner: '" + aligner + "' is not valid")
}
if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false))
@@ -278,10 +275,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Add bwa aln jobs */
- def addBwaAln(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addBwaAln(R1: File, R2: Option[File], output: File): File = {
val bwaAlnR1 = new BwaAln(this)
bwaAlnR1.fastq = R1
- bwaAlnR1.deps = deps
bwaAlnR1.output = swapExt(output.getParent, output, ".bam", ".R1.sai")
bwaAlnR1.isIntermediate = true
add(bwaAlnR1)
@@ -289,7 +285,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val samFile: File = if (paired) {
val bwaAlnR2 = new BwaAln(this)
bwaAlnR2.fastq = R2.get
- bwaAlnR2.deps = deps
bwaAlnR2.output = swapExt(output.getParent, output, ".bam", ".R2.sai")
bwaAlnR2.isIntermediate = true
add(bwaAlnR2)
@@ -324,41 +319,47 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Adds bwa mem jobs */
- def addBwaMem(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addBwaMem(R1: File, R2: Option[File], output: File): File = {
val bwaCommand = new BwaMem(this)
bwaCommand.R1 = R1
if (paired) bwaCommand.R2 = R2.get
- bwaCommand.deps = deps
bwaCommand.R = Some(getReadGroupBwa)
val sortSam = new SortSam(this)
sortSam.output = output
- add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
+ val pipe = bwaCommand | sortSam
+ pipe.isIntermediate = chunking || !skipMarkduplicates
+ pipe.threadsCorrection = -1
+ add(pipe)
output
}
- def addGsnap(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addGsnap(R1: File, R2: Option[File], output: File): File = {
+ val zcatR1 = extractIfNeeded(R1, output.getParentFile)
+ val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
val gsnapCommand = new Gsnap(this)
- gsnapCommand.input = if (paired) List(R1, R2.get) else List(R1)
- gsnapCommand.deps = deps
- gsnapCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
- gsnapCommand.isIntermediate = true
- add(gsnapCommand)
+ gsnapCommand.input = if (paired) List(zcatR1._2, zcatR2.get._2) else List(zcatR1._2)
+ gsnapCommand.output = swapExt(output.getParentFile, output, ".bam", ".sam")
val reorderSam = new ReorderSam(this)
reorderSam.input = gsnapCommand.output
- reorderSam.output = swapExt(output.getParent, output, ".sorted.bam", ".reordered.bam")
- add(reorderSam)
-
- addAddOrReplaceReadGroups(reorderSam.output, output)
+ reorderSam.output = swapExt(output.getParentFile, output, ".sorted.bam", ".reordered.bam")
+
+ val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
+ val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
+ Some(gsnapCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
+ pipe.threadsCorrection = -1
+ zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
+ zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
+ add(pipe)
+ ar._2
}
- def addTophat(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addTophat(R1: File, R2: Option[File], output: File): File = {
// TODO: merge mapped and unmapped BAM ~ also dealing with validation errors in the unmapped BAM
val tophat = new Tophat(this)
tophat.R1 = tophat.R1 :+ R1
if (paired) tophat.R2 = tophat.R2 :+ R2.get
tophat.output_dir = new File(outputDir, "tophat_out")
- tophat.deps = deps
// always output BAM
tophat.no_convert_bam = false
// and always keep input ordering
@@ -392,10 +393,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
reorderSam.output = swapExt(output.getParent, output, ".merge.bam", ".reordered.bam")
add(reorderSam)
- addAddOrReplaceReadGroups(reorderSam.output, output)
+ val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
+ add(ar._1)
+ ar._2
}
/** Adds stampy jobs */
- def addStampy(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addStampy(R1: File, R2: Option[File], output: File): File = {
var RG: String = "ID:" + readgroupId + ","
RG += "SM:" + sampleId.get + ","
@@ -410,10 +413,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val stampyCmd = new Stampy(this)
stampyCmd.R1 = R1
if (paired) stampyCmd.R2 = R2.get
- stampyCmd.deps = deps
stampyCmd.readgroup = RG
stampyCmd.sanger = true
- stampyCmd.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+ stampyCmd.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
stampyCmd.isIntermediate = true
add(stampyCmd)
val sortSam = SortSam(this, stampyCmd.output, output)
@@ -423,33 +425,54 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Adds bowtie jobs */
- def addBowtie(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
+ def addBowtie(R1: File, R2: Option[File], output: File): File = {
+ val zcatR1 = extractIfNeeded(R1, output.getParentFile)
+ val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
+ zcatR1._1.foreach(add(_))
+ zcatR2.foreach(_._1.foreach(add(_)))
val bowtie = new Bowtie(this)
- bowtie.R1 = R1
- if (paired) bowtie.R2 = R2
- bowtie.deps = deps
- bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+ bowtie.R1 = zcatR1._2
+ if (paired) bowtie.R2 = Some(zcatR2.get._2)
+ bowtie.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
bowtie.isIntermediate = true
- add(bowtie)
- addAddOrReplaceReadGroups(bowtie.output, output)
+ val ar = addAddOrReplaceReadGroups(bowtie.output, output)
+ val pipe = new BiopetFifoPipe(this, (Some(bowtie) :: Some(ar._1) :: Nil).flatten)
+ pipe.threadsCorrection = -1
+ add(pipe)
+ ar._2
}
/** Adds Star jobs */
- def addStar(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
- val starCommand = Star(this, R1, R2, outputDir, isIntermediate = true, deps = deps)
- add(starCommand)
- addAddOrReplaceReadGroups(starCommand.outputSam, output)
+ def addStar(R1: File, R2: Option[File], output: File): File = {
+ val zcatR1 = extractIfNeeded(R1, output.getParentFile)
+ val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
+ val starCommand = Star(this, zcatR1._2, zcatR2.map(_._2), outputDir, isIntermediate = true)
+ val ar = addAddOrReplaceReadGroups(starCommand.outputSam, output)
+ val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
+ Some(starCommand) :: Some(ar._1) :: Nil).flatten)
+ pipe.threadsCorrection = -1
+ zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
+ zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
+ add(pipe)
+ ar._2
}
/** Adds Start 2 pass jobs */
- def addStar2pass(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
- val starCommand = Star._2pass(this, R1, R2, outputDir, isIntermediate = true, deps = deps)
+ def addStar2pass(R1: File, R2: Option[File], output: File): File = {
+ val zcatR1 = extractIfNeeded(R1, output.getParentFile)
+ val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
+ zcatR1._1.foreach(add(_))
+ zcatR2.foreach(_._1.foreach(add(_)))
+
+ val starCommand = Star._2pass(this, zcatR1._2, zcatR2.map(_._2), outputDir, isIntermediate = true)
addAll(starCommand._2)
- addAddOrReplaceReadGroups(starCommand._1, output)
+ val ar = addAddOrReplaceReadGroups(starCommand._1, output)
+ add(ar._1)
+ ar._2
}
/** Adds AddOrReplaceReadGroups */
- def addAddOrReplaceReadGroups(input: File, output: File): File = {
+ def addAddOrReplaceReadGroups(input: File, output: File): (AddOrReplaceReadGroups, File) = {
val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, input, output)
addOrReplaceReadGroups.createIndex = true
@@ -461,9 +484,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (readgroupSequencingCenter.isDefined) addOrReplaceReadGroups.RGCN = readgroupSequencingCenter.get
if (readgroupDescription.isDefined) addOrReplaceReadGroups.RGDS = readgroupDescription.get
if (!skipMarkduplicates) addOrReplaceReadGroups.isIntermediate = true
- add(addOrReplaceReadGroups)
- addOrReplaceReadGroups.output
+ (addOrReplaceReadGroups, addOrReplaceReadGroups.output)
}
/** Returns readgroup for bwa */
@@ -488,22 +510,18 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
* @param runDir directory to extract when needed
* @return returns extracted file
*/
- def extractIfNeeded(file: File, runDir: File): File = {
- if (file == null) file
- else if (file.getName.endsWith(".gz") || file.getName.endsWith(".gzip")) {
+ def extractIfNeeded(file: File, runDir: File): (Option[BiopetCommandLineFunction], File) = {
+ require(file != null)
+ 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
+ (Some(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
+ (Some(pbzip2), newFile)
+ } else (None, 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 710ff17cb665d8bf41c4b1bb41eb7dceb9c81060..377c771cee17b62922381cd09d9c4ebd0aa15aec 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
@@ -18,13 +18,9 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-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.Fastqc
-import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
@@ -36,7 +32,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
*
* Created by pjvan_thof on 2/12/15.
*/
-class MappingTest extends TestNGSuite with Matchers {
+abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Mapping = {
new Mapping {
override def configName = "mapping"
@@ -48,15 +44,13 @@ class MappingTest extends TestNGSuite with Matchers {
@DataProvider(name = "mappingOptions")
def mappingOptions = {
- val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
val paired = Array(true, false)
- val chunks = Array(1, 5, 10, 100)
+ val chunks = Array(1, 5)
val skipMarkDuplicates = Array(true, false)
val skipFlexipreps = Array(true, false)
val zipped = Array(true, false)
for (
- aligner <- aligners;
pair <- paired;
chunk <- chunks;
skipMarkDuplicate <- skipMarkDuplicates;
@@ -91,28 +85,6 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
-
- //aligners
- 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)
- mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else if (aligner == "star-2pass") 3 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Bowtie]) shouldBe ((if (aligner == "bowtie") 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Stampy]) shouldBe ((if (aligner == "stampy") 1 else 0) * chunks)
-
- // Sort sam or replace readgroup
- val sort = aligner match {
- case "bwa-mem" | "bwa-aln" | "stampy" => "sortsam"
- case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
- case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
- }
-
- if (aligner != "tophat") { // FIXME
- //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)
- }
}
// remove temporary run directory all tests in the class have been run
@@ -121,7 +93,17 @@ class MappingTest extends TestNGSuite with Matchers {
}
}
+class MappingBwaMemTest extends AbstractTestMapping("bwa-mem")
+class MappingBwaAlnTest extends AbstractTestMapping("bwa-aln")
+class MappingStarTest extends AbstractTestMapping("star")
+class MappingStar2PassTest extends AbstractTestMapping("star-2pass")
+class MappingBowtieTest extends AbstractTestMapping("bowtie")
+class MappingStampyTest extends AbstractTestMapping("stampy")
+class MappingGsnapTest extends AbstractTestMapping("gsnap")
+class MappingTophatTest extends AbstractTestMapping("tophat")
+
object MappingTest {
+
val outputDir = Files.createTempDir()
new File(outputDir, "input").mkdirs()
diff --git a/public/pom.xml b/public/pom.xml
index cf2ea52f0c710db8abf2ce1c1202a7dd12d80dd0..0f2785691ad8dab0d8111a6204894b8801e4eeac 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -44,13 +44,14 @@
<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>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <scoverage.plugin.version>1.0.4</scoverage.plugin.version>
+ <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
+ <scalaVersion>2.10.4</scalaVersion>
</properties>
<build>
@@ -79,6 +80,7 @@
<version>2.18.1</version>
<configuration>
<forkCount>1C</forkCount>
+ <argLine>-Xmx300m</argLine>
<workingDirectory>${project.build.directory}</workingDirectory>
</configuration>
</plugin>
@@ -243,10 +245,12 @@
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
- <scalaVersion>2.10.2</scalaVersion>
+ <scalaVersion>${scalaVersion}</scalaVersion>
+ <aggregate>true</aggregate>
+ <highlighting>true</highlighting>
<!-- other parameters -->
</configuration>
- </plugin>
+ </plugin>
</plugins>
</build>
<reporting>
@@ -255,6 +259,17 @@
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
+ <configuration>
+ <aggregate>true</aggregate> <!-- for aggregated report -->
+ <highlighting>true</highlighting>
+ </configuration>
+ <reportSets>
+ <reportSet>
+ <reports>
+ <report>report</report> <!-- select only one report from: report, integration-report and report-only reporters -->
+ </reports>
+ </reportSet>
+ </reportSets>
</plugin>
</plugins>
</reporting>
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 2ee8c3b1930aff553234f6f3860d7c13e0818783..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
@@ -36,21 +36,22 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
var transcriptome: Option[File] = config("transcriptome")
var tagsLibrary: Option[File] = config("tags_library")
- override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
- "m" -> 1,
- "k" -> 1,
- "best" -> true,
- "strata" -> true,
- "seedmms" -> 1
- ), "mapping" -> Map(
- "aligner" -> "bowtie",
- "skip_flexiprep" -> true,
- "skip_markduplicates" -> true
- ), "flexiprep" -> Map(
- "skip_clip" -> true,
- "skip_trim" -> true
- ), "strandSensitive" -> true
- ), super.defaults)
+ override def defaults = Map(
+ "bowtie" -> Map(
+ "m" -> 1,
+ "k" -> 1,
+ "best" -> true,
+ "strata" -> true,
+ "seedmms" -> 1
+ ), "mapping" -> Map(
+ "aligner" -> "bowtie",
+ "skip_flexiprep" -> true,
+ "skip_markduplicates" -> true
+ ), "flexiprep" -> Map(
+ "skip_clip" -> true,
+ "skip_trim" -> true
+ ), "strandSensitive" -> true
+ )
def summaryFile: File = new File(outputDir, "Sage.summary.json")
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index f9cbddd1d75560c3c5e5c538a1ac0080dacd620a..26302af07fb2abac8007faaf9dbc55e16fca23e1 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -199,11 +199,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
val vcfFilter = new VcfFilter(qscript) {
override def configName = "vcffilter"
- override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
+ override def defaults = Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
"filter_ref_calls" -> true
- ), super.defaults)
+ )
}
vcfFilter.inputVcf = m2v.output
vcfFilter.outputVcf = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.filter.vcf.gz")
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 53286ecde3d44e4e6ad91fe142a5740b4909ceca..31777668d11df48a3ad99a663d60aad6e7666966 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
@@ -109,7 +109,6 @@ object ShivaTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
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 caeea0326d46e4b7673dae4a3d07f27c3cbd5f4e..dae0b974329950501369990e3a53bae077f8f071 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
@@ -112,7 +112,6 @@ object ShivaVariantcallingTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
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 7c3cc327858be60bb3d299e550c0f4244b656560..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
@@ -38,9 +38,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
inputFiles :+= new InputFile(inputVCF)
}
- override def defaults = ConfigUtils.mergeMaps(Map(
+ override def defaults = Map(
"varianteffectpredictor" -> Map("everything" -> true)
- ), super.defaults)
+ )
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
similarity index 100%
rename from public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
rename to public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
similarity index 100%
rename from public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
rename to public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
similarity index 100%
rename from public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
rename to public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
similarity index 100%
rename from public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
rename to public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
diff --git a/public/yamsvp/src/test/resources/log4j.properties b/public/yamsvp/src_old/test/resources/log4j.properties
similarity index 100%
rename from public/yamsvp/src/test/resources/log4j.properties
rename to public/yamsvp/src_old/test/resources/log4j.properties