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biopet.biopet
Commits
fe65dd17
Commit
fe65dd17
authored
Nov 09, 2016
by
Peter van 't Hof
Browse files
Added sanity checks for outputDir
parent
531c04b7
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
fe65dd17
...
...
@@ -38,6 +38,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if
(
config
.
contains
(
"output_dir"
,
path
=
Nil
))
config
(
"output_dir"
,
path
=
Nil
).
asFile
else
new
File
(
"."
)
}
require
(
outputDir
.
canRead
,
s
"No premision to read outputdir: $outputDir"
)
require
(
outputDir
.
canWrite
,
s
"No premision to read outputdir: $outputDir"
)
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
var
disableScatter
:
Boolean
=
false
...
...
@@ -67,6 +69,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
final
def
script
()
{
outputDir
=
config
(
"output_dir"
)
outputDir
=
outputDir
.
getAbsoluteFile
BiopetQScript
.
checkOutputDir
(
outputDir
)
init
()
biopetScript
()
logger
.
info
(
"Biopet script done"
)
...
...
@@ -153,4 +158,13 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
object
BiopetQScript
{
case
class
InputFile
(
file
:
File
,
md5
:
Option
[
String
]
=
None
)
def
checkOutputDir
(
outputDir
:
File
)
:
Unit
=
{
// Sanity checks
require
(
outputDir
.
getParentFile
.
canRead
,
s
"No premision to read parent of outputdir: ${outputDir.getParentFile}"
)
require
(
outputDir
.
getParentFile
.
canWrite
,
s
"No premision to write parent of outputdir: ${outputDir.getParentFile}"
)
outputDir
.
mkdir
()
require
(
outputDir
.
canRead
,
s
"No premision to read outputdir: $outputDir"
)
require
(
outputDir
.
canWrite
,
s
"No premision to write outputdir: $outputDir"
)
}
}
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
fe65dd17
...
...
@@ -77,6 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
val
pipelineName
=
this
.
getClass
.
getSimpleName
.
toLowerCase
.
split
(
"""\$"""
).
head
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"
)
logDir
.
mkdirs
()
new
File
(
logDir
,
"biopet."
+
BiopetQCommandLine
.
timestamp
+
".log"
)
...
...
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