Commit e28ecd68 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-546

parents 659e18de 6abbb191
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.generateindexes
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
......
......@@ -45,7 +45,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
@Test
def testNcbiAssembly(): Unit = {
val pipeline = initPipeline(Map())
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("ncbi_assembly_id" -> "id")))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("ncbi_assembly_report" -> "id")))
noException should be thrownBy pipeline.script()
}
......
......@@ -24,7 +24,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.gentrap.template
import java.io.File
......
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -24,7 +24,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import htsjdk.samtools.{ SAMSequenceDictionary, SamReaderFactory }
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import nl.lumc.sasc.biopet.core.Reference
......
......@@ -24,7 +24,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -35,6 +35,8 @@ import scala.collection.JavaConversions._
/**
* Created by pjvanthof on 18/12/15.
*
* This trait is meant to extend pipelines from that require a alignment step
*/
trait MultisampleMappingTrait extends MultiSampleQScript
with Reference { qscript: QScript =>
......@@ -65,7 +67,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
Some(report)
}
override def defaults = super.defaults ++ Map("reordersam" -> Map("allow_incomplete_dict_concordance" -> true))
override def defaults: Map[String, Any] = super.defaults ++ Map("reordersam" -> Map("allow_incomplete_dict_concordance" -> true))
override def fixedValues: Map[String, Any] = super.fixedValues ++ Map("gearssingle" -> Map("skip_flexiprep" -> true))
......@@ -101,7 +103,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy val bamToFastq: Boolean = config("bam_to_fastq", default = false)
lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
def keepFinalBamfile = samples(sampleId).libraries.size == 1
def keepFinalBamfile: Boolean = samples(sampleId).libraries.size == 1
lazy val mapping: Option[Mapping] = if (inputR1.isDefined || (inputBam.isDefined && bamToFastq)) {
val m: Mapping = new Mapping(qscript) {
......@@ -213,13 +215,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def summaryStats: Map[String, Any] = Map()
/** This is the merged bam file, None if the merged bam file is NA */
def bamFile = if (libraries.flatMap(_._2.bamFile).nonEmpty &&
def bamFile: Option[File] = if (libraries.flatMap(_._2.bamFile).nonEmpty &&
mergeStrategy != MultisampleMapping.MergeStrategy.None)
Some(new File(sampleDir, s"$sampleId.bam"))
else None
/** By default the preProcessBam is the same as the normal bamFile. A pipeline can extend this is there are preprocess steps */
def preProcessBam = bamFile
def preProcessBam: Option[File] = bamFile
/** Default is set to keep the merged files, user can set this in the config. To change the default this method can be overriden */
def keepMergedFiles: Boolean = config("keep_merged_files", default = true)
......@@ -278,7 +280,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
gears.outputDir = new File(sampleDir, "gears")
add(gears)
case "none" =>
case x => Logging.addError(s"${x} is not a valid value for 'mapping_to_gears'")
case x => Logging.addError(s"$x is not a valid value for 'mapping_to_gears'")
}
}
}
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.mapping.template
import java.io.File
......
......@@ -21,7 +21,7 @@
<groupId>nl.lumc.sasc</groupId>
<name>Biopet</name>
<packaging>pom</packaging>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<modules>
<module>gatk</module>
......
......@@ -24,7 +24,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.sage
import java.io.{ File, FileOutputStream }
......
......@@ -21,7 +21,7 @@
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.shiva.template
import java.io.File
......
......@@ -21,7 +21,7 @@
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
......@@ -24,7 +24,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
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