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biopet.biopet
Commits
ad73824f
Commit
ad73824f
authored
Sep 21, 2015
by
Peter van 't Hof
Browse files
Fix summary when --sample flag is used in multisample pipelines
parent
d5ae90cf
Changes
3
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
ad73824f
...
...
@@ -86,7 +86,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig
.
writeReport
(
qSettings
.
runName
,
new
File
(
outputDir
,
".log/"
+
qSettings
.
runName
))
else
Logging
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writeable, outputdir can not be created"
)
reportClass
.
foreach
(
add
(
_
))
this
match
{
case
q
:
MultiSampleQScript
if
(
q.onlySamples.nonEmpty
)
=>
logger
.
info
(
"Write summary is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
(
add
(
_
))
}
Logging
.
checkErrors
()
}
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
ad73824f
...
...
@@ -26,7 +26,7 @@ trait MultiSampleQScript extends SummaryQScript {
qscript
=>
@Argument
(
doc
=
"Only Sample"
,
shortName
=
"s"
,
required
=
false
,
fullName
=
"sample"
)
private
val
onlySamples
:
List
[
String
]
=
Nil
private
[
core
]
val
onlySamples
:
List
[
String
]
=
Nil
require
(
globalConfig
.
map
.
contains
(
"samples"
),
"No Samples found in config"
)
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
ad73824f
...
...
@@ -135,7 +135,11 @@ trait SummaryQScript extends BiopetQScript {
for
((
_
,
file
)
<-
this
.
summaryFiles
)
addChecksum
(
file
)
add
(
writeSummary
)
this
match
{
case
q
:
MultiSampleQScript
if
(
q.onlySamples.nonEmpty
)
=>
logger
.
info
(
"Write summary is skipped because sample flag is used"
)
case
_
=>
add
(
writeSummary
)
}
}
}
...
...
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