From d475e1dce93d63acf34b52cbe8bd52ec2c070669 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 24 Jun 2016 14:39:04 +0200
Subject: [PATCH] Clean up the possible run modes
---
.../biopet/pipelines/gentrap/GentrapTest.scala | 18 +++++-------------
1 file changed, 5 insertions(+), 13 deletions(-)
diff --git a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 2857c0d2e..fd6ad7736 100644
--- a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -71,10 +71,6 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
.toMap
)
- val validExpressionMeasures = Set(
- "fragments_per_gene", "fragments_per_exon", "base_counts",
- "cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
-
@DataProvider(name = "expMeasuresstrandProtocol")
def expMeasuresStrandProtocolProvider = {
@@ -89,27 +85,23 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
} yield makeSamplesConfig(sampleNum, libNum, libType)
val strandProtocols = Array("non_specific", "dutp")
- // get all possible combinations of expression measures
- val expressionMeasures = validExpressionMeasures
- //.subsets
- //.map(_.toList)
- .toArray
for {
sampleConfig <- sampleConfigs.toArray
- //expressionMeasure <- expressionMeasures
strandProtocol <- strandProtocols
- } yield Array(sampleConfig, List(expressionMeasure), strandProtocol)
+ removeRiboReads <- Array(true, false)
+ } yield Array(sampleConfig, List(expressionMeasure), strandProtocol, removeRiboReads)
}
@Test(dataProvider = "expMeasuresstrandProtocol")
- def testGentrap(sampleConfig: SamplesConfig, expMeasures: List[String], strandProtocol: String) = {
+ def testGentrap(sampleConfig: SamplesConfig, expMeasures: List[String], strandProtocol: String, removeRiboReads: Boolean) = {
val settings = Map(
"output_dir" -> GentrapTest.outputDir,
"gsnap" -> Map("db" -> "test", "dir" -> "test"),
"expression_measures" -> expMeasures,
- "strand_protocol" -> strandProtocol
+ "strand_protocol" -> strandProtocol,
+ "remove_ribosomal_reads" -> removeRiboReads
) ++ aligner.map("aligner" -> _)
val config = ConfigUtils.mergeMaps(settings ++ sampleConfig, Map(GentrapTest.executables.toSeq: _*))
val gentrap: Gentrap = initPipeline(config)
--
GitLab