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biopet.biopet
Commits
0d5df191
Commit
0d5df191
authored
Nov 08, 2015
by
Peter van 't Hof
Browse files
Fixed jobOutputFile
parent
10524ce8
Changes
2
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Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
0d5df191
...
...
@@ -78,6 +78,13 @@ trait BiopetQScript extends Configurable with GatkLogging {
case
f
:
ScatterGatherableFunction
=>
f
.
scatterCount
=
1
case
_
=>
}
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
(
add
(
_
))
}
for
(
function
<-
functions
)
function
match
{
case
f
:
BiopetCommandLineFunction
=>
f
.
preProcessExecutable
()
...
...
@@ -96,11 +103,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
else
if
(!
i
.
file
.
canRead
())
Logging
.
addError
(
s
"Input file can not be read: ${i.file}"
)
}
this
match
{
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used
"
)
ca
se
_
=>
reportClass
.
foreach
(
add
(
_
)
)
}
functions
.
filter
(
_
.
jobOutputFile
==
null
).
foreach
(
f
=>
{
if
(
f
.
jobOutputFile
==
null
&&
f
.
firstOutput
!=
null
)
f
.
jobOutputFile
=
new
File
(
f
.
firstOutput
.
getAbsoluteFile
.
getParent
,
"."
+
f
.
firstOutput
.
getName
+
"."
+
configName
+
".out
"
)
el
se
throw
new
IllegalStateException
(
s
"Can't generate a jobOutputFile for $f"
)
}
)
if
(
logger
.
isDebugEnabled
)
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
s
".log/${qSettings.runName}.deps.json"
))
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
View file @
0d5df191
...
...
@@ -58,9 +58,6 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
case
e
:
NullPointerException
=>
null
}
if
(
jobOutputFile
==
null
&&
firstOutput
!=
null
)
jobOutputFile
=
new
File
(
firstOutput
.
getAbsoluteFile
.
getParent
,
"."
+
firstOutput
.
getName
+
"."
+
configName
+
".out"
)
nCoresRequest
=
Option
(
threads
)
/** The 1e retry does not yet upgrade the memory */
...
...
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