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biopet.biopet
Commits
42b34355
Commit
42b34355
authored
Dec 06, 2016
by
Peter van 't Hof
Browse files
Fixing dir names
parent
7d530c20
Changes
3
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
42b34355
...
...
@@ -104,7 +104,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
_
=>
}
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
BiopetQCommandLine
.
timestamp
)
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
qSettings
.
runName
.
toLowerCase
)
if
(
outputDir
.
getParentFile
.
canWrite
||
(
outputDir
.
exists
&&
outputDir
.
canWrite
))
globalConfig
.
writeReport
(
new
File
(
logDir
,
"config"
))
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
42b34355
...
...
@@ -77,7 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
val
pipelineConfig
=
globalConfig
.
map
.
getOrElse
(
pipelineName
,
Map
()).
asInstanceOf
[
Map
[
String
,
Any
]]
val
pipelineOutputDir
=
new
File
(
globalConfig
.
map
.
getOrElse
(
"output_dir"
,
pipelineConfig
.
getOrElse
(
"output_dir"
,
"./"
)).
toString
)
BiopetQScript
.
checkOutputDir
(
pipelineOutputDir
)
val
logDir
:
File
=
new
File
(
pipelineOutputDir
,
".log"
+
File
.
separator
+
BiopetQCommandLine
.
timestamp
)
val
logDir
:
File
=
new
File
(
pipelineOutputDir
,
".log"
+
File
.
separator
+
pipelineName
+
"."
+
BiopetQCommandLine
.
timestamp
)
logDir
.
mkdirs
()
val
logFile
=
new
File
(
logDir
,
"biopet.log"
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
42b34355
...
...
@@ -50,6 +50,7 @@ object WriteDependencies extends Logging with Configurable {
* @param outputDir
*/
def
writeDependencies
(
functions
:
Seq
[
QFunction
],
outputDir
:
File
)
:
Unit
=
{
outputDir
.
mkdirs
()
logger
.
info
(
"Start calculating dependencies"
)
val
errorOnMissingInput
:
Boolean
=
config
(
"error_on_missing_input"
,
false
)
...
...
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