Commit b733ff34 authored by Peter van 't Hof's avatar Peter van 't Hof

Removed out commented tests

parent ea03623c
......@@ -74,8 +74,6 @@ class ShivaTest extends TestNGSuite with Matchers {
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
//pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
//pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
// Gatk preprocess
......
......@@ -79,12 +79,6 @@ class FlexiprepTest extends TestNGSuite with Matchers {
else if (paired && !(skipClip && skipTrim)) 4
else if (!paired && !(skipClip && skipTrim)) 2)
flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
//flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) if (paired) 2 else 1 else 0)
//flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
//flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
//flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (paired) 1 else 0)
//flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 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
......
......@@ -91,16 +91,8 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
//mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (!zipped || (chunks > 1 && skipFlexiprep)) 0 else if (paired) 2 else 1)
//mapping.functions.count(_.isInstanceOf[SeqStat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * (chunks + 1))
//mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
//mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
//mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
//mapping.functions.count(_.isInstanceOf[Sickle]) shouldBe ((if (skipFlexiprep) 0 else 1) * chunks)
//mapping.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipFlexiprep) 0 else if (paired) 2 else 1)
//aligners
//mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa-mem") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") if (paired) 2 else 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") if (paired) 1 else 0 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") if (paired) 0 else 1 else 0) * chunks)
......
......@@ -62,7 +62,6 @@ class ShivaTest extends TestNGSuite with Matchers {
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
"single_sample_variantcalling" -> single,
"library_variantcalling" -> library), m)
}
if (!sample1 && !sample2 && !sample3) { // When no samples
......@@ -76,8 +75,6 @@ class ShivaTest extends TestNGSuite with Matchers {
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
//pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
//pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0) +
......
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