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biopet.biopet
Commits
eb605a1f
Commit
eb605a1f
authored
Feb 08, 2016
by
Wai Yi Leung
Browse files
Merge branch 'fix-268' into 'develop'
Fix 268 Fixes #268 See merge request !318
parents
acbbc173
e16d2e05
Changes
2
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
eb605a1f
...
...
@@ -23,9 +23,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
org.broadinstitute.gatk.utils.commandline.Argument
/** Base for biopet pipeline */
trait
BiopetQScript
extends
Configurable
with
GatkLogging
{
qscript
:
QScript
=>
...
...
@@ -99,7 +97,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
inputFiles
.
foreach
{
i
=>
if
(!
i
.
file
.
exists
())
Logging
.
addError
(
s
"Input file does not exist: ${i.file}"
)
else
if
(!
i
.
file
.
canRead
)
Logging
.
addError
(
s
"Input file can not be read: ${i.file}"
)
if
(!
i
.
file
.
canRead
)
Logging
.
addError
(
s
"Input file can not be read: ${i.file}"
)
if
(!
i
.
file
.
isAbsolute
)
Logging
.
addError
(
s
"Input file should be an absulute path: ${i.file}"
)
}
functions
.
filter
(
_
.
jobOutputFile
==
null
).
foreach
(
f
=>
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
View file @
eb605a1f
...
...
@@ -39,7 +39,7 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
var
vcfSampleList
:
Option
[
File
]
=
config
(
"vcf_sample_list"
)
var
variants
:
Option
[
Int
]
=
config
(
"variants"
)
override
def
defaultCoreMemory
=
6
.0
override
def
defaultCoreMemory
=
8
.0
override
def
beforeGraph
()
:
Unit
=
{
val
validValues
:
Set
[
Int
]
=
Set
(
0
,
1
)
...
...
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