Commit cdfcea81 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-582

parents e826cd20 7812d950
...@@ -17,10 +17,14 @@ node('local') { ...@@ -17,10 +17,14 @@ node('local') {
} }
} }
stage('Report tests') { stage('Report Tests') {
junit '*/target/surefire-reports/*.xml' junit '*/target/surefire-reports/*.xml'
} }
stage('Check Documentation') {
sh 'mkdocs build --clean --strict'
}
if(currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) { if(currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
currentBuild.result = "SUCCESS" currentBuild.result = "SUCCESS"
slackSend (color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc') slackSend (color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
......
...@@ -14,7 +14,7 @@ Full documantation is here: [Biopet documantation](http://biopet-docs.readthedoc ...@@ -14,7 +14,7 @@ Full documantation is here: [Biopet documantation](http://biopet-docs.readthedoc
Biopet is available as a JAR package in SHARK. The easiest way to start using it is to activate the `biopet` environment module, which sets useful aliases and environment variables: Biopet is available as a JAR package in SHARK. The easiest way to start using it is to activate the `biopet` environment module, which sets useful aliases and environment variables:
~~~ ~~~
$ module load biopet/v0.6.0 $ module load biopet/v0.8.0
~~~ ~~~
With each Biopet release, an accompanying environment module is also released. The latest release is version 0.4.0, thus `biopet/v0.4.0` is the module you would want to load. With each Biopet release, an accompanying environment module is also released. The latest release is version 0.4.0, thus `biopet/v0.4.0` is the module you would want to load.
......
...@@ -26,7 +26,7 @@ ...@@ -26,7 +26,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </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.basty package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{ File, FileOutputStream } import java.io.{ File, FileOutputStream }
......
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
......
...@@ -93,15 +93,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -93,15 +93,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
} }
logger.info("Running pre commands") logger.info("Running pre commands")
for (function <- functions) function match { var count = 0
case f: BiopetCommandLineFunction => for (function <- functions) {
f.preProcessExecutable() function match {
f.beforeGraph() case f: BiopetCommandLineFunction =>
f.internalBeforeGraph() f.preProcessExecutable()
f.commandLine f.beforeGraph()
case f: WriteSummary => f.init() f.internalBeforeGraph()
case _ => f.commandLine
case f: WriteSummary => f.init()
case _ =>
}
count += 1
if (count % 500 == 0) logger.info(s"Preprocessing done for ${count} jobs out of ${functions.length} total")
} }
logger.info(s"Preprocessing done for ${functions.length} functions")
val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase) val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
...@@ -116,6 +122,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -116,6 +122,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}") if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
} }
logger.info("Set stdout file when not set")
functions.filter(_.jobOutputFile == null).foreach(f => { functions.filter(_.jobOutputFile == null).foreach(f => {
val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
BiopetQScript.safeOutputs(f) match { BiopetQScript.safeOutputs(f) match {
...@@ -127,6 +134,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -127,6 +134,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (!skipWriteDependencies) WriteDependencies.writeDependencies( if (!skipWriteDependencies) WriteDependencies.writeDependencies(
functions, functions,
new File(logDir, "graph")) new File(logDir, "graph"))
else logger.debug("Write dependencies is skipped")
Logging.checkErrors() Logging.checkErrors()
logger.info("Script complete without errors") logger.info("Script complete without errors")
......
/**
* 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.core package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
/**
* 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.core package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
...@@ -116,11 +116,11 @@ object WriteDependencies extends Logging with Configurable { ...@@ -116,11 +116,11 @@ object WriteDependencies extends Logging with Configurable {
case s: WriteSummary if s.qscript.root == null => true case s: WriteSummary if s.qscript.root == null => true
case _ => false case _ => false
}), "intermediate" -> f.isIntermediate, }), "intermediate" -> f.isIntermediate,
"depends_on_intermediate" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).exists(files(_).isIntermediate), "depends_on_intermediate" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
"depends_on_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct, "depends_on_jobs" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,
"output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct, "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct,
"outputs" -> (f.jobOutputFile :: BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList), "outputs" -> (f.jobOutputFile :: BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList),
"inputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList, "inputs" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).toList,
"done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList, "done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList,
"fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList, "fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList,
"stdout_file" -> f.jobOutputFile, "stdout_file" -> f.jobOutputFile,
......
/**
* 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.core package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
/**
* 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.core.annotation package nl.lumc.sasc.biopet.core.annotation
import java.io.File import java.io.File
......
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <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.
#
import argparse import argparse
from os.path import join from os.path import join
......
/**
* 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.extensions package nl.lumc.sasc.biopet.extensions
import java.io.File import java.io.File
......
/**
* 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.extensions package nl.lumc.sasc.biopet.extensions
import java.io.File import java.io.File
......
/**
* 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.extensions.centrifuge package nl.lumc.sasc.biopet.extensions.centrifuge
import java.io.File import java.io.File
......
/**
* 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.extensions.centrifuge package nl.lumc.sasc.biopet.extensions.centrifuge
import java.io.File import java.io.File
......
...@@ -41,11 +41,6 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with ...@@ -41,11 +41,6 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
@Argument(doc = "What kind of analysis to run: DEL,DUP,INV,TRA") @Argument(doc = "What kind of analysis to run: DEL,DUP,INV,TRA")
var analysistype: String = _ var analysistype: String = _
override def beforeGraph(): Unit = {
super.beforeGraph()
deps ::= new File(input.getParentFile, input.getName + ".bai")
}
def cmdLine = required(executable) + def cmdLine = required(executable) +
required("-t", analysistype) + required("-t", analysistype) +
required("-o", outputvcf) + required("-o", outputvcf) +
......
/**
* 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.extensions.gatk package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
......
...@@ -137,7 +137,6 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter ...@@ -137,7 +137,6 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) + optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) + optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) + optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") + optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") + repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") + optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
...@@ -146,7 +145,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter ...@@ -146,7 +145,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") + optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") + conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") + conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
} }
object GenotypeGVCFs { object GenotypeGVCFs {
......
...@@ -453,7 +453,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt ...@@ -453,7 +453,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) + optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) + optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) + optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") + optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") + repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") + optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
...@@ -512,7 +511,12 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt ...@@ -512,7 +511,12 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-mmq", min_mapping_quality_score, spaceSeparated = true, escape = true, format = "%s") + optional("-mmq", min_mapping_quality_score, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") + conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") + conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
} }
object HaplotypeCaller { object HaplotypeCaller {
......
...@@ -300,7 +300,6 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat ...@@ -300,7 +300,6 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) + optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) + optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) + optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") + optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") + repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") + optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
...@@ -323,7 +322,12 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat ...@@ -323,7 +322,12 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") + repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") + conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") + conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
} }
object UnifiedGenotyper { object UnifiedGenotyper {
......
/**
* 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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.extensions.xhmm