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biopet.biopet
Commits
ea210687
Commit
ea210687
authored
Jan 30, 2015
by
Sander van der Zeeuw
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fixed output_dir name bug
parent
1d0235fe
Changes
3
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3 changed files
with
19 additions
and
9 deletions
+19
-9
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+9
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+3
-2
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+7
-5
No files found.
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
ea210687
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.core.config.
{
Config
ValueIndex
,
Config
,
Configurable
}
import
org.broadinstitute.gatk.utils.commandline.Argument
import
org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
...
...
@@ -29,7 +29,14 @@ trait BiopetQScript extends Configurable with GatkLogging {
@Argument
(
doc
=
"JSON config file(s)"
,
fullName
=
"config_file"
,
shortName
=
"config"
,
required
=
false
)
val
configfiles
:
List
[
File
]
=
Nil
var
outputDir
:
String
=
_
var
outputDir
:
String
=
{
val
temp
=
Config
.
getValueFromMap
(
Config
.
global
.
map
,
ConfigValueIndex
(
this
.
configName
,
configPath
,
"output_dir"
))
if
(
temp
.
isEmpty
)
throw
new
IllegalArgumentException
(
"No output_dir defined in config"
)
else
{
val
t
=
temp
.
get
.
value
.
toString
if
(!
t
.
endsWith
(
"/"
))
t
+
"/"
else
t
}
}
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
var
disableScatter
:
Boolean
=
false
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
ea210687
...
...
@@ -108,7 +108,7 @@ trait MultiSampleQScript extends BiopetQScript {
def
createFile
(
suffix
:
String
)
=
new
File
(
sampleDir
,
sampleId
+
suffix
)
/** Returns sample directory */
def
sampleDir
=
outputDir
+
"samples"
+
File
.
pathSeparator
+
sampleId
+
File
.
pathS
eparator
def
sampleDir
=
outputDir
+
"samples"
+
File
.
separator
+
sampleId
+
File
.
s
eparator
}
/** Sample type, need implementation in pipeline */
...
...
@@ -130,7 +130,8 @@ trait MultiSampleQScript extends BiopetQScript {
}
/**
* Runs addAndTrackJobs method for each sample */
* Runs addAndTrackJobs method for each sample
*/
final
def
addSamplesJobs
()
{
for
((
sampleId
,
sample
)
<-
samples
)
{
sample
.
addAndTrackJobs
()
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
ea210687
...
...
@@ -80,6 +80,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
merge
.
sortOrder
=
"coordinate"
merge
.
output
=
bamFile
add
(
merge
)
//TODO: Add BigWIg track
}
val
macs2
=
new
Macs2CallPeak
(
qscript
)
...
...
@@ -103,13 +105,13 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
addSamplesJobs
for
((
sampleId
,
sample
)
<-
samples
)
{
for
(
control
<-
sample
.
controls
)
{
if
(!
samples
.
contains
(
control
))
throw
new
IllegalStateException
(
"For sample: "
+
sampleId
+
" this control: "
+
control
+
" does not exist"
)
for
(
control
Id
<-
sample
.
controls
)
{
if
(!
samples
.
contains
(
control
Id
))
throw
new
IllegalStateException
(
"For sample: "
+
sampleId
+
" this control: "
+
control
Id
+
" does not exist"
)
val
macs2
=
new
Macs2CallPeak
(
this
)
macs2
.
treatment
=
sample
.
bamFile
macs2
.
control
=
samples
(
control
).
bamFile
macs2
.
name
=
sample
+
"_VS_"
+
control
macs2
.
control
=
samples
(
control
Id
).
bamFile
macs2
.
name
=
sample
Id
+
"_VS_"
+
controlId
macs2
.
outputdir
=
sample
.
sampleDir
+
"/"
+
"macs2/"
+
macs2
.
name
+
"/"
add
(
macs2
)
}
...
...
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