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biopet.biopet
Commits
2f92eb6d
Commit
2f92eb6d
authored
Oct 29, 2015
by
Peter van 't Hof
Browse files
Fixed summary file name
parent
11fe02b4
Changes
6
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
View file @
2f92eb6d
...
...
@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/** Extension for Kraken */
class
Kraken
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
View file @
2f92eb6d
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.sambamba
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
/** General Sambamba extension */
abstract
class
Sambamba
extends
BiopetCommandLineFunction
with
Version
{
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
View file @
2f92eb6d
...
...
@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* KrakenReportToJson function class for usage in Biopet pipelines
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
View file @
2f92eb6d
...
...
@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools
* Created by wyleung on 25-9-15.
*/
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
import
nl.lumc.sasc.biopet.utils.ToolCommand
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
2f92eb6d
...
...
@@ -16,11 +16,11 @@
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -158,7 +158,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
}
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"
x"
)
+
"-"
+
libId
.
getOrElse
(
"x
"
)
+
".gears.summary.json"
)
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"
sampleName_unknown
"
)
+
".gears.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
.
empty
...
...
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @
2f92eb6d
...
...
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
KrakenReportToJson
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
...
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