Commit 86e7d090 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add settings

parent 8acebe9a
......@@ -73,8 +73,10 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
Some(gears)
}
protected var skipFlexiprep: Boolean = config("skip_flexiprep", default = false)
protected def executeFlexiprep(r1: File, r2: Option[File]): (File, Option[File]) = {
if (!config("skip_flexiprep", default = false).asBoolean) {
if (!skipFlexiprep) {
val flexiprep = new Flexiprep(this)
flexiprep.input_R1 = r1
flexiprep.input_R2 = r2
......@@ -129,7 +131,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".gears.summary.json")
/** Pipeline settings shown in the summary file */
def summarySettings: Map[String, Any] = Map.empty
def summarySettings: Map[String, Any] = Map(
"skip_flexiprep" -> skipFlexiprep,
"gears_use_kraken" -> krakenScript.isDefined,
"gear_use_qiime_rtax" -> qiimeRatx.isDefined,
"gear_use_qiime_closed" -> qiimeClosed.isDefined
)
/** Statistics shown in the summary file */
def summaryFiles: Map[String, File] = Map.empty ++
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment