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biopet.biopet
Commits
0a33b3d3
Commit
0a33b3d3
authored
Jul 15, 2014
by
Peter van 't Hof
Browse files
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Update to Queue/GATK 3.2
parent
719894d1
Changes
53
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53 changed files
with
107 additions
and
103 deletions
+107
-103
.gitignore
.gitignore
+3
-1
bam-metrics/pom.xml
bam-metrics/pom.xml
+1
-1
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+1
-1
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+1
-1
biopet-framework/pom.xml
biopet-framework/pom.xml
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+3
-3
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
...n/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
+11
-11
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+3
-3
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala
...n/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala
+3
-3
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
.../scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
+4
-4
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala
...n/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
...ork/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
...work/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
+2
-2
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
.../src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
...lumc/sasc/biopet/function/PythonCommandLineFunction.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
...src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
...lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
...umc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
...lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
...mc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala
...asc/biopet/function/picard/CollectInsertSizeMetrics.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
.../nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
...in/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
+1
-1
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
...lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
+1
-1
flexiprep/pom.xml
flexiprep/pom.xml
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
...n/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
...ain/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
...ain/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+5
-5
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
...c/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
.../biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
...biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
...umc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
...c/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
+1
-1
gatk-genotyping/pom.xml
gatk-genotyping/pom.xml
+1
-1
gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+4
-4
gatk-variantcalling/pom.xml
gatk-variantcalling/pom.xml
+1
-1
gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+6
-6
gatk/pom.xml
gatk/pom.xml
+1
-1
gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+13
-12
mapping/pom.xml
mapping/pom.xml
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
...ain/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
...in/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+7
-7
pipeline-template/pom.xml
pipeline-template/pom.xml
+1
-1
pipeline-template/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/PipelineTemplate.scala
...c/sasc/biopet/pipelines/bammetrics/PipelineTemplate.scala
+3
-3
pom.xml
pom.xml
+1
-0
No files found.
.gitignore
View file @
0a33b3d3
...
...
@@ -4,4 +4,6 @@
/pipeline-template/nbactions.xml
/gatk-variantcalling/nbactions.xml
/gatk-variantcalling/dependency-reduced-pom.xml
/bam-metrics/nbactions.xml
\ No newline at end of file
/bam-metrics/nbactions.xml
dependency-reduced-pom.xml
nbactions.xml
bam-metrics/pom.xml
View file @
0a33b3d3
...
...
@@ -55,7 +55,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
org.broadinstitute.
sting
.queue.QScript
import
org.broadinstitute.
gatk
.queue.QScript
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.apps.
{
BedToInterval
,
BiopetFlagstat
}
...
...
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
CoverageStats
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
biopet-framework/pom.xml
View file @
0a33b3d3
...
...
@@ -52,7 +52,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.core
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
scala.sys.process._
import
nl.lumc.sasc.biopet.core.config._
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
0a33b3d3
...
...
@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.queue.QException
import
org.broadinstitute.
sting
.queue.function.CommandLineFunction
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk
.queue.QException
import
org.broadinstitute.
gatk
.queue.function.CommandLineFunction
import
org.broadinstitute.
gatk.utils
.commandline._
import
scala.sys.process._
import
scala.util.matching.Regex
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.core
import
org.broadinstitute.
sting
.queue.function.JavaCommandLineFunction
import
org.broadinstitute.
gatk
.queue.function.JavaCommandLineFunction
abstract
class
BiopetJavaCommandLineFunction
extends
JavaCommandLineFunction
with
BiopetCommandLineFunctionTrait
{
executeble
=
"java"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
View file @
0a33b3d3
...
...
@@ -27,21 +27,21 @@
package
nl.lumc.sasc.biopet.core
import
java.io.File
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
sting
.queue.util._
import
org.broadinstitute.
sting
.queue.QCommandPlugin
import
org.broadinstitute.
sting
.queue.QScript
import
org.broadinstitute.
sting
.queue.QScriptManager
import
org.broadinstitute.
sting
.queue.engine.
{
QStatusMessenger
,
QGraphSettings
,
QGraph
}
import
org.broadinstitute.
gatk.utils
.commandline._
import
org.broadinstitute.
gatk
.queue.util._
import
org.broadinstitute.
gatk
.queue.QCommandPlugin
import
org.broadinstitute.
gatk
.queue.QScript
import
org.broadinstitute.
gatk
.queue.QScriptManager
import
org.broadinstitute.
gatk
.queue.engine.
{
QStatusMessenger
,
QGraphSettings
,
QGraph
}
import
collection.JavaConversions._
import
org.broadinstitute.
sting
.utils.classloader.PluginManager
import
org.broadinstitute.
sting
.utils.exceptions.UserException
import
org.broadinstitute.
sting
.utils.io.IOUtils
import
org.broadinstitute.
sting
.utils.help.ApplicationDetails
import
org.broadinstitute.
gatk
.utils.classloader.PluginManager
import
org.broadinstitute.
gatk
.utils.exceptions.UserException
import
org.broadinstitute.
gatk
.utils.io.IOUtils
import
org.broadinstitute.
gatk
.utils.help.ApplicationDetails
import
java.io.FileOutputStream
import
java.net.URL
import
java.util.
{
ResourceBundle
,
Arrays
}
import
org.broadinstitute.
sting
.utils.text.TextFormattingUtils
import
org.broadinstitute.
gatk
.utils.text.TextFormattingUtils
import
org.apache.commons.io.FilenameUtils
/**
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
0a33b3d3
...
...
@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
sting
.queue.QSettings
import
org.broadinstitute.
sting
.queue.function.QFunction
import
org.broadinstitute.
gatk.utils
.commandline._
import
org.broadinstitute.
gatk
.queue.QSettings
import
org.broadinstitute.
gatk
.queue.function.QFunction
trait
BiopetQScript
extends
Configurable
{
@Argument
(
doc
=
"Config Json file"
,
shortName
=
"config"
,
required
=
false
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
0a33b3d3
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.FileOutputStream
//import org.broadinstitute.sting.queue.QCommandLine
import
org.broadinstitute.
sting
.queue.util.Logging
import
org.broadinstitute.
gatk
.queue.util.Logging
trait
PipelineCommand
extends
Logging
{
// val src = ""
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.core.apps
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMSequenceRecord
import
java.io.File
import
net.sf.samtools.SAMSequenceRecord
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
}
import
java.io.PrintWriter
import
net.sf.samtools.SAMFileReader
import
scala.io.Source
class
BedToInterval
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.core.apps
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMRecord
import
java.io.
{
BufferedInputStream
,
File
,
FileInputStream
,
PrintWriter
}
import
net.sf.samtools.SAMFileReader
import
net.sf.samtools.SAMRecord
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
scala.io.Source
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
}
import
org.broadinstitute.
sting
.queue.util.Logging
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
}
import
org.broadinstitute.
gatk
.queue.util.Logging
import
scala.collection.JavaConversions._
import
scala.collection.mutable.Map
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala
View file @
0a33b3d3
...
...
@@ -5,7 +5,7 @@ import java.util.zip.GZIPInputStream
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
scala.io.Source
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
}
class
FastqSplitter
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
javaMainClass
=
getClass
.
getName
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.config
import
nl.lumc.sasc.biopet.core._
import
scala.util.parsing.json._
import
java.io.File
import
org.broadinstitute.
sting
.queue.util.Logging
import
org.broadinstitute.
gatk
.queue.util.Logging
class
Config
(
var
map
:
Map
[
String
,
Any
])
extends
Logging
{
logger
.
debug
(
"Init phase of config"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.core.config
import
java.io.File
import
org.broadinstitute.
sting
.queue.util.Logging
import
org.broadinstitute.
gatk
.queue.util.Logging
trait
Configurable
extends
Logging
{
val
root
:
Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
class
Cat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
View file @
0a33b3d3
...
...
@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.function
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.queue.function.InProcessFunction
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk
.queue.function.InProcessFunction
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
import
scala.sys.process._
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
//import org.broadinstitute.sting.queue.function.CommandLineFunction
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
class
Pbzip2
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import
java.io.FileOutputStream
import
nl.lumc.sasc.biopet.core._
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
import
scala.collection.JavaConversions._
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
class
Sha1sum
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline._
import
org.broadinstitute.
gatk.utils
.commandline._
import
java.io.File
class
Zcat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.function.bedtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
,
Argument
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
BedtoolsCoverage
(
val
root
:
Configurable
)
extends
Bedtools
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.function.bedtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
,
Argument
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
BedtoolsIntersect
(
val
root
:
Configurable
)
extends
Bedtools
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
class
CalculateHsMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"net.sf.picard.analysis.directed.CalculateHsMetrics"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
class
CollectGcBiasMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"net.sf.picard.analysis.CollectGcBiasMetrics"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
class
CollectInsertSizeMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"net.sf.picard.analysis.CollectInsertSizeMetrics"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
class
MarkDuplicates
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"net.sf.picard.sam.MarkDuplicates"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.function.picard
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
trait
Picard
extends
BiopetJavaCommandLineFunction
{
@Argument
(
doc
=
"VERBOSITY"
,
required
=
false
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
View file @
0a33b3d3
package
nl.lumc.sasc.biopet.function.samtools
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.
sting
.commandline.
{
Input
,
Output
}
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
}
import
java.io.File
class
SamtoolsFlagstat
(
val
root
:
Configurable
)
extends
Samtools
{
...
...
flexiprep/pom.xml
View file @
0a33b3d3
...
...
@@ -50,7 +50,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
import
scala.io.Source._
import
scala.sys.process._
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
import
scala.sys.process._
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
View file @
0a33b3d3
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function.fastq
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
import
scala.io.Source._
import
scala.sys.process._
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
0a33b3d3
...
...
@@ -4,12 +4,12 @@ import nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function._
import
nl.lumc.sasc.biopet.function.fastq._
import
org.broadinstitute.
sting
.queue.QScript
import
org.broadinstitute.
sting
.queue.extensions.gatk._
import
org.broadinstitute.
sting
.queue.extensions.picard._
import
org.broadinstitute.
sting
.queue.function._
import
org.broadinstitute.
gatk
.queue.QScript
import
org.broadinstitute.
gatk
.queue.extensions.gatk._
import
org.broadinstitute.
gatk
.queue.extensions.picard._
import
org.broadinstitute.
gatk
.queue.function._
import
scala.util.parsing.json._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
View file @
0a33b3d3
...
...
@@ -4,7 +4,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
FastqSync
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
FastqcToContams
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
FastqcToQualtype
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
Seqstat
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
View file @
0a33b3d3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
Summarize
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
gatk-genotyping/pom.xml
View file @
0a33b3d3
...
...
@@ -50,7 +50,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
0a33b3d3
...
...
@@ -3,10 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function._
import
org.broadinstitute.
sting
.queue.QScript
import
org.broadinstitute.
sting
.queue.extensions.gatk.
{
CommandLineGATK
,
GenotypeGVCFs
,
SelectVariants
}
import
org.broadinstitute.
sting
.queue.function._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
gatk
.queue.QScript
import
org.broadinstitute.
gatk
.queue.extensions.gatk.
{
CommandLineGATK
,
GenotypeGVCFs
,
SelectVariants
}
import
org.broadinstitute.
gatk
.queue.function._
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
class
GatkGenotyping
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
gatk-variantcalling/pom.xml
View file @
0a33b3d3
...
...
@@ -50,7 +50,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
0a33b3d3
...
...
@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.function._
import
org.broadinstitute.
sting
.queue.QScript
import
org.broadinstitute.
sting
.queue.extensions.gatk.
{
BaseRecalibrator
,
CommandLineGATK
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
GenotypeGVCFs
,
AnalyzeCovariates
}
import
org.broadinstitute.
sting
.queue.function._
import
org.broadinstitute.
sting
.commandline.
_
import
org.broadinstitute.
sting
.utils.variant.GATKVCFIndexType
import
org.broadinstitute.
gatk
.queue.QScript
import
org.broadinstitute.
gatk
.queue.extensions.gatk.
{
BaseRecalibrator
,
CommandLineGATK
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
GenotypeGVCFs
,
AnalyzeCovariates
}
import
org.broadinstitute.
gatk
.queue.function._
import
org.broadinstitute.
gatk.utils
.commandline.
{
Input
,
Output
,
Argument
}
import
org.broadinstitute.
gatk
.utils.variant.GATKVCFIndexType
class
GatkVariantcalling
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
@@ -126,7 +126,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
// GVCF options
if
(
gvcfMode
)
{
this
.
emitRefConfidence
=
org
.
broadinstitute
.
sting
.
gatk
.
walkers
.
haplotypecaller
.
HaplotypeCaller
.
ReferenceConfidenceMode
.
GVCF
this
.
emitRefConfidence
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
haplotypecaller
.
ReferenceConfidenceMode
.
GVCF
this
.
variant_index_type
=
GATKVCFIndexType
.
LINEAR
this
.
variant_index_parameter
=
128000
}
...
...
gatk/pom.xml
View file @
0a33b3d3
...
...
@@ -60,7 +60,7 @@
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
<artifactId>
queue-package
</artifactId>
<version>
3.
1
</version>
<version>
3.
2
</version>
</dependency>
</dependencies>
<build>
...
...
gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
View file @
0a33b3d3
...
...
@@ -2,18 +2,19 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.function._
import
nl.lumc.sasc.biopet.function.aligners._
import
java.io.File
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.pipelines.mapping._
import
nl.lumc.sasc.biopet.function.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep._
import
org.broadinstitute.sting.queue.QScript
import
org.broadinstitute.sting.queue.extensions.gatk._
import
org.broadinstitute.sting.queue.extensions.picard._
import
org.broadinstitute.sting.queue.function._
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk._
import
org.broadinstitute.gatk.queue.extensions.picard._
import
org.broadinstitute.gatk.queue.function._
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
}
import
scala.util.parsing.json._
import
org.broadinstitute.sting.utils.variant.GATKVCFIndexType
class
Gatk
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
def
this
()
=
this
(
null
)
...
...
@@ -150,7 +151,7 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
this
.
out
=
swapExt
(
dir
,
inputBam
,
".bam"
,
".split.bam"
)
this
.
read_filter
:+=
"ReassignMappingQuality"
this
.
U
=
org
.
broadinstitute
.
sting
.
gatk
.
arguments
.
ValidationExclusion
.
TYPE
.
ALLOW_N_CIGAR_READS
this
.
U
=
org
.
broadinstitute
.
gatk
.
engine
.
arguments
.
ValidationExclusion
.
TYPE
.
ALLOW_N_CIGAR_READS
}
add
(
splitNCigarReads
)
...
...
@@ -167,8 +168,8 @@ class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
this
.
memoryLimit
=
this
.
nct
*
2
// GVCF options
this
.
emitRefConfidence
=
org
.
broadinstitute
.
sting
.
gatk
.
walkers
.
haplotypecaller
.
HaplotypeCaller
.
ReferenceConfidenceMode
.
GVCF
this
.
variant_index_type
=
GATKVCFIndexType
.
LINEAR