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biopet.biopet
Commits
29f9b30f
Commit
29f9b30f
authored
Feb 03, 2015
by
Peter van 't Hof
Browse files
Name change
parent
5f8a8375
Changes
6
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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
29f9b30f
...
...
@@ -56,7 +56,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
add
Per
SampleJobs
()
addSample
s
Jobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
29f9b30f
...
...
@@ -151,7 +151,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
def
biopetScript
()
:
Unit
=
{
add
Per
SampleJobs
addSample
s
Jobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
29f9b30f
...
...
@@ -128,7 +128,7 @@ trait MultiSampleQScript extends BiopetQScript {
protected
def
sampleIds
:
Set
[
String
]
=
ConfigUtils
.
any2map
(
Config
.
global
.
map
(
"samples"
)).
keySet
/** Runs addAndTrackJobs method for each sample */
final
def
add
Per
SampleJobs
()
{
final
def
addSample
s
Jobs
()
{
if
(
onlySamples
.
isEmpty
)
{
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
addAndTrackJobs
()
}
addMultiSampleJobs
()
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
29f9b30f
...
...
@@ -102,7 +102,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
// Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
logger
.
info
(
"Starting CArP pipeline"
)
add
Per
SampleJobs
addSample
s
Jobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
View file @
29f9b30f
...
...
@@ -30,7 +30,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
}
def
biopetScript
()
{
this
.
addPer
SampleJobs
()
add
Sample
s
Jobs
()
}
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
29f9b30f
...
...
@@ -151,7 +151,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
tagsLibrary
=
cdl
.
output
}
add
Per
SampleJobs
addSample
s
Jobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
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