Commit 287c3a7e authored by Peter van 't Hof's avatar Peter van 't Hof

Adding main job to deps.json

parent d0bfad15
......@@ -36,6 +36,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
var executable: String = _
def mainFunction = false
/** This is the default shell for drmaa jobs */
def defaultRemoteCommand = "bash"
private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)
......
......@@ -110,6 +110,9 @@ object WriteDependencies extends Logging with Configurable {
name -> Map("command" -> (f match {
case cmd: CommandLineFunction => cmd.commandLine
case _ => None
}), "main_job" -> (f match {
case cmd: BiopetCommandLineFunction => cmd.mainFunction
case _ => false
}), "intermediate" -> f.isIntermediate,
"depends_on_intermediate" -> f.inputs.exists(files(_).isIntermediate),
"depends_on_jobs" -> f.inputs.toList.flatMap(files(_).outputJobNames).distinct,
......
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