From 86e7d090bc046ddb24f19eaacb0845c63b440bf8 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Dec 2015 14:22:43 +0100
Subject: [PATCH] Add settings
---
.../sasc/biopet/pipelines/gears/GearsSingle.scala | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index 02f35d7c5..e966e2371 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -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 ++
--
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