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biopet.biopet
Commits
5800e9ae
Commit
5800e9ae
authored
Dec 17, 2016
by
Peter van 't Hof
Browse files
Added a print of final config
parent
92a0c676
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
5800e9ae
...
...
@@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.utils.
{
Question
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
/**
* Created by pjvanthof on 17/12/2016.
...
...
@@ -27,7 +28,9 @@ trait TemplateTool extends ToolCommand {
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
standard
:
Map
[
String
,
Any
]
=
Map
(
"output_dir"
->
Question
.
askValue
(
"Output directory"
,
validation
=
List
(
isAbsolutePath
,
parentIsWritable
)))
pipelineMap
(
standard
,
cmdArgs
.
expert
)
val
config
=
pipelineMap
(
standard
,
cmdArgs
.
expert
)
println
(
ConfigUtils
.
mapToYaml
(
config
))
}
def
pipelineMap
(
map
:
Map
[
String
,
Any
],
expert
:
Boolean
)
:
Map
[
String
,
Any
]
...
...
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