Commit d475e1dc authored by Wai Yi Leung's avatar Wai Yi Leung

Clean up the possible run modes

parent b55361cd
......@@ -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)
......
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