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biopet.biopet
Commits
a1f5260d
Commit
a1f5260d
authored
Mar 02, 2015
by
Peter van 't Hof
Browse files
Format change
parent
e3b3e129
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
a1f5260d
...
...
@@ -22,9 +22,7 @@ import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
}
/**
* This trait creates a structured way of use multisample pipelines
*/
/** This trait creates a structured way of use multisample pipelines */
trait
MultiSampleQScript
extends
SummaryQScript
{
qscript
=>
...
...
@@ -41,19 +39,12 @@ trait MultiSampleQScript extends SummaryQScript {
/** Overrules config of qscript with default sample */
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
)
/**
* Library class with basic functions build in
* @param libId
*/
/** Library class with basic functions build in */
abstract
class
AbstractLibrary
(
val
libId
:
String
)
extends
Summarizable
{
/** Overrules config of qscript with default sample and default library */
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
,
defaultLibrary
=
libId
)
/**
* Name overules the one from qscript
* @param summarizable
* @param name
*/
/** Name overules the one from qscript */
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
)
:
Unit
=
{
qscript
.
addSummarizable
(
summarizable
,
name
,
Some
(
sampleId
),
Some
(
libId
))
}
...
...
@@ -162,7 +153,7 @@ trait MultiSampleQScript extends SummaryQScript {
}
/**
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
.
*/
def
addMultiSampleJobs
()
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
View file @
a1f5260d
...
...
@@ -11,16 +11,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*/
trait
Summarizable
{
/**
* Must return files to store into summary
* @return
*/
/** Must return files to store into summary */
def
summaryFiles
:
Map
[
String
,
File
]
/**
* Must returns stats to store into summary
* @return
*/
/** Must returns stats to store into summary */
def
summaryStats
:
Map
[
String
,
Any
]
/**
...
...
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