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biopet.biopet
Commits
b733ff34
Commit
b733ff34
authored
Oct 05, 2015
by
Peter van 't Hof
Browse files
Removed out commented tests
parent
ea03623c
Changes
4
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protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
b733ff34
...
...
@@ -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
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
b733ff34
...
...
@@ -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
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
b733ff34
...
...
@@ -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
)
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
b733ff34
...
...
@@ -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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