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biopet.biopet
Commits
ea781d9b
Commit
ea781d9b
authored
Nov 20, 2015
by
Peter van 't Hof
Browse files
Remove addSummaryJobs()
parent
89b7a259
Changes
2
Hide whitespace changes
Inline
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
ea781d9b
...
...
@@ -133,12 +133,11 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
that
:
SummaryQScript
=>
that
.
init
()
that
.
biopetScript
()
that
.
addSummaryJobs
()
this
match
{
case
s
:
SummaryQScript
=>
s
.
addSummaryQScript
(
that
)
case
_
=>
}
case
that
:
BiopetQScript
=>
case
that
:
BiopetQScript
=>
that
.
init
()
that
.
biopetScript
()
case
_
=>
subPipeline
.
script
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
ea781d9b
...
...
@@ -92,8 +92,11 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
summaryQScripts
:+=
summaryQScript
}
private
var
addedJobs
=
false
/** Add jobs to qscript to execute summary, also add checksum jobs */
def
addSummaryJobs
()
:
Unit
=
{
if
(
addedJobs
)
throw
new
IllegalStateException
(
"Summary jobs for this QScript are already executed"
)
val
writeSummary
=
new
WriteSummary
(
this
)
def
addChecksum
(
file
:
File
)
:
Unit
=
{
...
...
@@ -160,6 +163,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
logger
.
info
(
"Write summary is skipped because sample flag is used"
)
case
_
=>
add
(
writeSummary
)
}
addedJobs
=
true
}
}
...
...
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