Commit 0e122e1f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added docs

parent 46df370a
...@@ -54,6 +54,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -54,6 +54,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
writer.close() writer.close()
} }
/**
* This value is used to let you job wait a x number of second after it finish.
* This is ionly used when having storage delay issues
*/
var jobDelayTime: Option[Int] = config("job_delay_time") var jobDelayTime: Option[Int] = config("job_delay_time")
// This overrides the default "sh" from queue. For Biopet the default is "bash" // This overrides the default "sh" from queue. For Biopet the default is "bash"
...@@ -168,6 +172,15 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -168,6 +172,15 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
this this
} }
/**
* This method can handle args that have multiple args for 1 arg name
* @param argName Name of the arg like "-h" or "--help"
* @param values Values for this arg
* @param groupSize Values must come in groups of x number, default is 1
* @param minGroups Minimal groups that are required, default is 0, when 0 the method return en empty string
* @param maxGroups Max number of groups that can be filled here
* @return Command part of this arg
*/
def multiArg(argName: String, values: Iterable[Any], groupSize: Int = 1, minGroups: Int = 0, maxGroups: Int = 0): String = { def multiArg(argName: String, values: Iterable[Any], groupSize: Int = 1, minGroups: Int = 0, maxGroups: Int = 0): String = {
if (values.size % groupSize != 0) if (values.size % groupSize != 0)
Logging.addError(s"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}") Logging.addError(s"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}")
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