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biopet.biopet
Commits
dc6dc49c
Commit
dc6dc49c
authored
Mar 10, 2017
by
Peter van 't Hof
Committed by
GitHub
Mar 10, 2017
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Merge pull request #35 from biopet/fix-BIOPET-538
Test fail on format/git issues
parents
527d43b8
1edaf174
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-3
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+3
-3
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Jenkinsfile
View file @
dc6dc49c
...
...
@@ -22,6 +22,10 @@ node('local') {
junit
'*/target/surefire-reports/*.xml'
}
stage
(
'Check git on changes'
)
{
sh
'if [ $(git diff | wc -l) -eq 0 ]; then true; else echo "[ERROR] Git is not clean anymore after build"; git diff; echo "[ERROR] This might be caused by reformated code, if so run maven locally"; false; fi'
}
stage
(
'Check Documentation'
)
{
sh
'mkdocs build --clean --strict'
}
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
dc6dc49c
...
...
@@ -15,10 +15,10 @@
package
nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.nio.file.
{
Files
,
Paths
}
import
java.nio.file.
{
Files
,
Paths
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.tools.vcfstats.
{
SampleStats
,
SampleToSampleStats
,
Stats
,
VcfStats
}
import
nl.lumc.sasc.biopet.tools.vcfstats.
{
SampleStats
,
SampleToSampleStats
,
Stats
,
VcfStats
}
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
...
...
@@ -170,7 +170,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val
vcf
=
resourcePath
(
"/chrQ.vcf.gz"
)
val
ref
=
resourcePath
(
"/fake_chrQ.fa"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
))
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
))
}
@Test
...
...
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