Commit 02733716 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed testing

parent d4e45996
......@@ -45,8 +45,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def summaryFiles: Map[String, File] = {
Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
(if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
if (!skipTrim || !skipClip)
Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
(if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
else Map("input_R1" -> input_R1) ++
(if (paired) Map("input_R2" -> input_R2.get) else Map())
}
/** returns settings to store in summary */
......
......@@ -84,7 +84,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else if (paired) 1 else 0)
flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipClip && skipTrim) 0 else if (paired) 2 else 1)
}
// remove temporary run directory all tests in the class have been run
......
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