diff --git a/.gitignore b/.gitignore
index 5fd45143edf282ef15ab630694347ffce6286919..5b3b383c070f15ec77b88bd28e379e6628fb8e78 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,4 @@
dependency-reduced-pom.xml
*~
*.swp
-/Biopet/nbproject/private/
-/Biopet/build/
\ No newline at end of file
+test/
diff --git a/biopet-framework/nb-configuration.xml b/biopet-framework/nb-configuration.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d5d1f5902742b129f6f2220b537520a4312cf133
--- /dev/null
+++ b/biopet-framework/nb-configuration.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-shared-configuration>
+ <!--
+This file contains additional configuration written by modules in the NetBeans IDE.
+The configuration is intended to be shared among all the users of project and
+therefore it is assumed to be part of version control checkout.
+Without this configuration present, some functionality in the IDE may be limited or fail altogether.
+-->
+ <config-data xmlns="http://www.netbeans.org/ns/maven-config-data/1">
+ <configurations>
+ <configuration id="yamsvp" profiles=""/>
+ </configurations>
+ </config-data>
+ <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
+ <!--
+Properties that influence various parts of the IDE, especially code formatting and the like.
+You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
+That way multiple projects can share the same settings (useful for formatting rules for example).
+Any value defined here will override the pom.xml file value but is only applicable to the current project.
+-->
+ <netbeans.hint.license>apache20</netbeans.hint.license>
+ <com-junichi11-netbeans-changelf.enable>true</com-junichi11-netbeans-changelf.enable>
+ <com-junichi11-netbeans-changelf.use-project>true</com-junichi11-netbeans-changelf.use-project>
+ <com-junichi11-netbeans-changelf.lf-kind>CRLF</com-junichi11-netbeans-changelf.lf-kind>
+ <com-junichi11-netbeans-changelf.use-global>false</com-junichi11-netbeans-changelf.use-global>
+ </properties>
+</project-shared-configuration>
diff --git a/biopet-framework/nbactions-yamsvp.xml b/biopet-framework/nbactions-yamsvp.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3e0fc37dc34358aabb70d312672ea3f587ca458c
--- /dev/null
+++ b/biopet-framework/nbactions-yamsvp.xml
@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+ <action>
+ <actionName>run</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+ </goals>
+ <properties>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir ../test -config ../test/samples.json -run</exec.args>
+ <exec.executable>java</exec.executable>
+ <exec.workingdir>../test</exec.workingdir>
+ </properties>
+ </action>
+ <action>
+ <actionName>debug</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+ </goals>
+ <properties>
+ <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir ../test -config ../test/samples.json -run</exec.args>
+ <exec.executable>java</exec.executable>
+ <jpda.listen>true</jpda.listen>
+ <exec.workingdir>../test</exec.workingdir>
+ </properties>
+ </action>
+ <action>
+ <actionName>profile</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+ </goals>
+ <properties>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir ../test -config ../test/samples.json -run</exec.args>
+ <exec.executable>java</exec.executable>
+ <exec.workingdir>../test</exec.workingdir>
+ </properties>
+ </action>
+ </actions>
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
new file mode 100644
index 0000000000000000000000000000000000000000..6bb36d42e3d49ed78e0e37534b74c20f26f017eb
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
@@ -0,0 +1,80 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.extensions.svcallers
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument , MissingArgumentException}
+import java.io.File
+
+class Clever(val root: Configurable) extends BiopetCommandLineFunction {
+ executable = config("exe", default = "clever")
+
+ private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
+
+ override val defaultVmem = "4G"
+ override val defaultThreads = 8
+
+ override def versionCommand = versionexecutable.getAbsolutePath
+ override val versionRegex = """(.*)""".r
+
+
+ @Input(doc = "Input file (bam)")
+ var input: File = _
+
+ @Input(doc = "Reference Fasta file")
+ var reference: File = _
+
+ @Argument(doc = "Work directory")
+ var workdir: String = _
+
+ @Output(doc = "Clever VCF output")
+ lazy val outputvcf: File = {
+ new File(workdir + "predictions.vcf")
+ }
+
+ @Output(doc = "Clever raw output")
+ lazy val outputraw: File = {
+ new File(workdir + "predictions.raw.txt")
+ }
+
+// var vcf: File = output
+ if ( reference == null ) reference = config("reference")
+
+
+// var T: Option[Int] = config("T", default = defaultThreads)
+ var f: Boolean = config("f", default = true) // delete work directory before running
+// var w: String = config("w", default = workdir + "/work")
+ var a: Boolean = config("a", default = false) // don't recompute AS tags
+ var k: Boolean = config("k", default = false) // keep working directory
+ var r: Boolean = config("r", default = false) // take read groups into account
+
+ override def beforeCmd {
+ if (workdir == null) throw new Exception("Clever :: Workdirectory is not defined")
+// if (input.getName.endsWith(".sort.bam")) sorted = true
+ }
+
+ def cmdLine = required(executable) +
+ optional("-T", nCoresRequest) +
+ conditional(f ,"-f") +
+ conditional(a ,"-a") +
+ conditional(k, "-k") +
+ conditional(r ,"-r") +
+ required(this.input) +
+ required(this.reference) +
+ required(this.workdir)
+}
+
+object Clever {
+ def apply(root: Configurable, input: File, reference: File, runDir: String): Clever = {
+ val clever = new Clever(root)
+ clever.input = input
+ clever.reference = reference
+ clever.workdir = runDir
+ return clever
+ }
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 98e77d7b0b398027abf46744e70b72b9437b0b05..ec9fa67323a962873fa82dab2321cda58203d88f 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -5,22 +5,17 @@
package nl.lumc.sasc.biopet.pipelines.yamsvp
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.extensions.Cat
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+import nl.lumc.sasc.biopet.extensions.svcallers.Clever
-import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.scripts.PrefixFastq
-
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._
-import org.broadinstitute.gatk.utils.commandline.{ Argument }
-
@@ -30,9 +25,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
var reference: File = _
var finalBamFiles: List[File] = Nil
- @Input(doc = "countBed", required = false)
- var countBed : File = _
-
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
reference = config("reference", required = true)
@@ -47,8 +39,9 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// start with QC, alignment, call sambamba, call sv callers, reporting
// read config and set all parameters for the pipeline
- logger.warn("runSamplesJobs")
+ logger.info("Starting YAM SV Pipeline")
runSamplesJobs
+ //
}
@@ -59,7 +52,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val sampleID: String = sampleConfig("ID").toString
val sampleDir: String = outputDir + sampleID + "/"
for ((library, libraryFiles) <- runLibraryJobs(sampleConfig)) {
- libraryFastqFiles +:= libraryFiles("prefix_fastq")
libraryBamfiles +:= libraryFiles("FinalBam")
}
@@ -75,7 +67,13 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
add(cat)
cat.output
} else null
-
+
+ /// bamfile will be used as input for the SV callers. First run Clever
+// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
+//
+// val clever = Clever(this, bamFile, this.reference, sampleDir )
+// outputFiles += ("CleverVCF" -> List(clever.outputvcf) )
+// add(clever)
return outputFiles
}
@@ -86,29 +84,12 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val sampleID: String = sampleConfig("ID").toString
val runDir: String = outputDir + sampleID + "/run_" + runID + "/"
if (runConfig.contains("R1")) {
- val flexiprep = new Flexiprep(this)
- flexiprep.outputDir = runDir + "flexiprep/"
- flexiprep.input_R1 = new File(runConfig("R1").toString)
- flexiprep.skipClip = true
- flexiprep.skipTrim = true
- flexiprep.sampleName = sampleID
- flexiprep.libraryName = runID
- flexiprep.init
- flexiprep.biopetScript
- addAll(flexiprep.functions)
-
- val flexiprepOutput = for ((key,file) <- flexiprep.outputFiles if key.endsWith("output_R1")) yield file
- val prefixFastq = PrefixFastq.apply(this, flexiprepOutput.head, runDir)
- prefixFastq.prefix = config("sage_tag", default = "CATG")
- prefixFastq.deps +:= flexiprep.outputFiles("fastq_input_R1")
- add(prefixFastq)
- outputFiles += ("prefix_fastq" -> prefixFastq.output)
-
- val mapping = new Mapping(this)
- mapping.skipFlexiprep = true
+ val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir)
+ mapping.skipFlexiprep = false
mapping.skipMarkduplicates = true
mapping.defaultAligner = "bwa"
- mapping.input_R1 = prefixFastq.output
+ mapping.chunking = true
+ mapping.numberChunks = 4
mapping.RGLB = runConfig("ID").toString
mapping.RGSM = sampleConfig("ID").toString
if (runConfig.contains("PL")) mapping.RGPL = runConfig("PL").toString
@@ -118,12 +99,12 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.init
mapping.biopetScript
addAll(mapping.functions)
-
+
outputFiles += ("FinalBam" -> mapping.outputFiles("finalBamFile"))
} else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
+ logger.debug( outputFiles )
return outputFiles
}
-
}
object Yamsvp extends PipelineCommand {