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biopet.biopet
Commits
36333df3
Commit
36333df3
authored
Jan 23, 2017
by
Sander Bollen
Committed by
GitHub
Jan 23, 2017
Browse files
Merge pull request #10 from biopet/fix-BIOPET-534
Fix biopet 534
parents
2467bc10
51f0b19d
Changes
6
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
36333df3
...
...
@@ -19,7 +19,6 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
WriteSummary
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.function.QFunction
...
...
@@ -118,11 +117,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
functions
.
filter
(
_
.
jobOutputFile
==
null
).
foreach
(
f
=>
{
try
{
val
className
=
if
(
f
.
getClass
.
isAnonymousClass
)
f
.
getClass
.
getSuperclass
.
getSimpleName
else
f
.
getClass
.
getSimpleName
f
.
jobOutputFile
=
new
File
(
f
.
firstOutput
.
getAbsoluteFile
.
getParent
,
"."
+
f
.
firstOutput
.
getName
+
"."
+
className
+
".out"
)
}
catch
{
case
e
:
NullPointerException
=>
logger
.
warn
(
s
"Can't generate a jobOutputFile for $f"
)
val
className
=
if
(
f
.
getClass
.
isAnonymousClass
)
f
.
getClass
.
getSuperclass
.
getSimpleName
else
f
.
getClass
.
getSimpleName
BiopetQScript
.
safeOutputs
(
f
)
match
{
case
Some
(
o
)
=>
f
.
jobOutputFile
=
new
File
(
o
.
head
.
getAbsoluteFile
.
getParent
,
"."
+
f
.
firstOutput
.
getName
+
"."
+
className
+
".out"
)
case
_
=>
f
.
jobOutputFile
=
new
File
(
"./stdout"
)
// Line is here for test backup
}
})
...
...
@@ -159,7 +157,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
that
:
BiopetQScript
=>
that
.
init
()
that
.
biopetScript
()
case
_
=>
subPipeline
.
script
case
_
=>
subPipeline
.
script
()
}
addAll
(
subPipeline
.
functions
)
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
36333df3
...
...
@@ -101,6 +101,9 @@ object WriteDependencies extends Logging with Configurable {
file
.
addOutputJob
(
function
)
files
+=
output
->
file
}
val
file
=
files
.
getOrElse
(
function
.
jobOutputFile
,
QueueFile
(
function
.
jobOutputFile
))
file
.
addOutputJob
(
function
)
files
+=
function
.
jobOutputFile
->
file
}
val
jobs
=
functionNames
.
par
.
map
{
...
...
@@ -116,7 +119,7 @@ object WriteDependencies extends Logging with Configurable {
"depends_on_intermediate"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
exists
(
files
(
_
).
isIntermediate
),
"depends_on_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
.
flatMap
(
files
(
_
).
outputJobNames
).
distinct
,
"output_used_by_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
.
flatMap
(
files
(
_
).
inputJobNames
).
distinct
,
"outputs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
,
"outputs"
->
(
f
.
jobOutputFile
::
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
)
,
"inputs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
,
"done_files"
->
BiopetQScript
.
safeDoneFiles
(
f
).
getOrElse
(
Seq
()).
toList
,
"fail_files"
->
BiopetQScript
.
safeFailFiles
(
f
).
getOrElse
(
Seq
()).
toList
,
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
36333df3
...
...
@@ -40,10 +40,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
vepScript
:
String
=
config
(
"vep_script"
)
@Input
(
doc
=
"input VCF"
,
required
=
true
)
var
input
:
File
=
null
var
input
:
File
=
_
@Output
(
doc
=
"output file"
,
required
=
true
)
var
output
:
File
=
null
var
output
:
File
=
_
override
def
subPath
=
{
if
(
vepVersion
.
isSet
)
super
.
subPath
++
List
(
"vep_settings"
)
++
vepVersion
()
...
...
@@ -160,7 +160,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override
def
defaultCoreMemory
=
4.0
@Output
private
var
_summary
:
File
=
null
private
var
_summary
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
...
...
@@ -312,11 +312,11 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
(
for
((
header
,
headerIndex
)
<-
headers
)
yield
{
val
name
=
header
.
stripPrefix
(
"["
).
stripSuffix
(
"]"
)
name
.
replaceAll
(
" "
,
"_"
)
->
(
contents
.
drop
(
headerIndex
+
1
).
takeWhile
(!
isHeader
(
_
)).
flatMap
{
line
=>
name
.
replaceAll
(
" "
,
"_"
)
->
contents
.
drop
(
headerIndex
+
1
).
takeWhile
(!
isHeader
(
_
)).
flatMap
{
line
=>
val
values
=
line
.
split
(
"\t"
,
2
)
if
(
values
.
last
.
isEmpty
||
values
.
last
==
"-"
)
None
else
Some
(
values
.
head
.
replaceAll
(
" "
,
"_"
)
->
tryToParseNumber
(
values
.
last
).
getOrElse
(
values
.
last
))
}.
toMap
)
}.
toMap
}).
toMap
}
}
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
View file @
36333df3
...
...
@@ -6,6 +6,7 @@ import org.testng.annotations.Test
/**
* Created by Sander Bollen on 12-10-16.
* Here we test utils
*/
class
UtilsTest
extends
TestNGSuite
with
Matchers
{
...
...
biopet-utils/src/test/scala/VcfUtilsTest.scala
→
biopet-utils/src/test/scala/
nl/lumc/sasc/biopet/utils/
VcfUtilsTest.scala
View file @
36333df3
import
htsjdk.variant.variantcontext.
{
Allele
,
Genotype
,
GenotypeBuilder
}
package
nl.lumc.sasc.biopet.utils
import
htsjdk.variant.variantcontext.
{
Allele
,
GenotypeBuilder
}
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.utils.VcfUtils
/**
* Created by Sander Bollen on 4-10-16.
*/
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
36333df3
...
...
@@ -50,7 +50,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
val
insertsizeExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"metrics"
).
values
.
exists
(
_
!=
Some
(
None
))
val
mappingExecuted
=
summary
.
getLibraryValues
(
"mapping"
).
nonEmpty
val
mappingExecuted
=
summary
.
getLibraryValues
(
"mapping"
).
exists
(
_
.
_2
.
isDefined
)
val
pairedFound
=
!
mappingExecuted
||
summary
.
getLibraryValues
(
"mapping"
,
"settings"
,
"paired"
).
exists
(
_
.
_2
==
Some
(
true
))
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
exists
{
case
((
sample
,
lib
),
value
)
=>
value
.
isDefined
}
...
...
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