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biopet.biopet
Commits
83e1c12f
Commit
83e1c12f
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Fixed unit test
parent
a50fc782
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
83e1c12f
...
...
@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.core.BiopetPipe
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
...
...
@@ -105,6 +106,8 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
outputName
shouldBe
(
if
(
inputMode
==
Some
(
"bam"
))
"bamfile"
else
"R1"
)
}
val
pipesJobs
=
gears
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetPipe
]).
flatMap
(
_
.
asInstanceOf
[
BiopetPipe
].
pipesJobs
)
gears
.
summarySettings
(
"gears_use_kraken"
)
shouldBe
kraken
.
getOrElse
(
true
)
gears
.
summarySettings
(
"gear_use_qiime_rtax"
)
shouldBe
qiimeRtax
gears
.
summarySettings
(
"gear_use_qiime_closed"
)
shouldBe
qiimeClosed
...
...
@@ -126,7 +129,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReportToJson
])
shouldBe
((
if
(
kraken
.
getOrElse
(
true
))
1
else
0
)
+
(
if
(
centrifuge
)
2
else
0
))
gears
.
function
s
.
count
(
_
.
isInstanceOf
[
Centrifuge
])
shouldBe
(
if
(
centrifuge
)
1
else
0
)
pipesJob
s
.
count
(
_
.
isInstanceOf
[
Centrifuge
])
shouldBe
(
if
(
centrifuge
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
CentrifugeKreport
])
shouldBe
(
if
(
centrifuge
)
2
else
0
)
}
}
...
...
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