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biopet.biopet
Commits
beef0cec
Commit
beef0cec
authored
Sep 27, 2015
by
Peter van 't Hof
Browse files
Hide null pointen from unit tests
parent
6bad7eaf
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
beef0cec
...
...
@@ -59,7 +59,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun
=
{
case
jt
:
JobTemplate
=>
jt
.
setRemoteCommand
(
remoteCommand
)
case
jt
:
JobTemplate
=>
jt
.
setRemoteCommand
(
remoteCommand
)
}
/**
...
...
@@ -304,8 +304,12 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
}
case
Right
(
cmd
)
=>
{
cmd
.
_outputAsStdout
=
true
if
(
cmd
.
outputs
!=
null
)
outputFiles
++=
cmd
.
outputs
if
(
cmd
.
inputs
!=
null
)
deps
++=
cmd
.
inputs
try
{
if
(
cmd
.
outputs
!=
null
)
outputFiles
++=
cmd
.
outputs
if
(
cmd
.
inputs
!=
null
)
deps
++=
cmd
.
inputs
}
catch
{
case
e
:
NullPointerException
=>
}
s
"'${prefix}' <( ${cmd.commandLine} ) "
}
}
...
...
@@ -319,8 +323,12 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
}
case
Right
(
cmd
)
=>
{
cmd
.
_inputAsStdin
=
true
if
(
cmd
.
outputs
!=
null
)
outputFiles
++=
cmd
.
outputs
if
(
cmd
.
inputs
!=
null
)
deps
++=
cmd
.
inputs
try
{
if
(
cmd
.
outputs
!=
null
)
outputFiles
++=
cmd
.
outputs
if
(
cmd
.
inputs
!=
null
)
deps
++=
cmd
.
inputs
}
catch
{
case
e
:
NullPointerException
=>
}
s
"'${prefix}' >( ${cmd.commandLine} ) "
}
}
...
...
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