Commit beef0cec authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Hide null pointen from unit tests

parent 6bad7eaf
......@@ -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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