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biopet.biopet
Commits
b34b4b44
Commit
b34b4b44
authored
Nov 21, 2016
by
Peter van 't Hof
Browse files
Explict test noException
parent
4fa9758a
Changes
1
Hide whitespace changes
Inline
Side-by-side
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @
b34b4b44
...
...
@@ -46,21 +46,21 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
def
testNcbiAssembly
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"ncbi_assembly_id"
->
"id"
)))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
def
testSingleFasta
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
)))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
def
testMultiFasta
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
List
(
"uri"
,
"uri2"
,
"uri3.gz"
))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -68,7 +68,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"dbsnp"
->
Map
(
"version"
->
Map
(
"vcf_uri"
->
"uri.vcf.gz"
)))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -76,7 +76,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"dbsnp"
->
Map
(
"version"
->
Map
(
"vcf_uri"
->
"uri.vcf.gz"
,
"contig_map"
->
Map
(
"1"
->
"chr1"
))))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -84,7 +84,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"dbsnp"
->
Map
(
"version"
->
Map
(
"vcf_uri"
->
"uri.vcf"
,
"contig_map"
->
Map
(
"1"
->
"chr1"
))))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -92,7 +92,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"dbsnp"
->
Map
(
"version"
->
Map
((
"vcf_uri"
->
"uri.vcf"
))))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -100,7 +100,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"dbsnp"
->
Map
(
"version"
->
Map
(
"vcf_uri"
->
List
(
"uri.vcf.gz"
,
"uri2.vcf.gz"
))))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -108,7 +108,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"vep"
->
Map
(
"version"
->
Map
(
"cache_uri"
->
"something/human_vep_80_hg19.tar.gz"
)))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -116,7 +116,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"gene_annotation"
->
Map
(
"version"
->
Map
(
"gtf_uri"
->
"bla.gf.gz"
)))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -124,7 +124,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"gene_annotation"
->
Map
(
"version"
->
Map
(
"gtf_uri"
->
"bla.gf"
)))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
@Test
...
...
@@ -132,7 +132,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val
pipeline
=
initPipeline
(
Map
(
"download_annotations"
->
true
))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
,
"gene_annotation"
->
Map
(
"version"
->
Map
(
"gff_uri"
->
"bla.gf"
)))))
pipeline
.
script
()
noException
should
be
thrownBy
pipeline
.
script
()
}
}
...
...
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