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biopet.biopet
Commits
b8da950d
Commit
b8da950d
authored
Sep 27, 2016
by
Peter van 't Hof
Browse files
Fixing code warning
parent
2b20899f
Changes
1
Hide whitespace changes
Inline
Side-by-side
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @
b8da950d
...
...
@@ -36,7 +36,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testNoFastaUri
:
Unit
=
{
def
testNoFastaUri
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
""
->
""
)))
intercept
[
IllegalArgumentException
]
{
...
...
@@ -45,28 +45,28 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testNcbiAssembly
:
Unit
=
{
def
testNcbiAssembly
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"ncbi_assembly_id"
->
"id"
)))
pipeline
.
script
()
}
@Test
def
testSingleFasta
:
Unit
=
{
def
testSingleFasta
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
"uri"
)))
pipeline
.
script
()
}
@Test
def
testMultiFasta
:
Unit
=
{
def
testMultiFasta
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"fasta_uri"
->
List
(
"uri"
,
"uri2"
,
"uri3.gz"
))))
pipeline
.
script
()
}
@Test
def
testSingleDbsnp
:
Unit
=
{
def
testSingleDbsnp
()
:
Unit
=
{
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"
)))))
...
...
@@ -74,7 +74,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testContigMapDbsnp
:
Unit
=
{
def
testContigMapDbsnp
()
:
Unit
=
{
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"
))))))
...
...
@@ -82,7 +82,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testUnzippedContigMapDbsnp
:
Unit
=
{
def
testUnzippedContigMapDbsnp
()
:
Unit
=
{
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"
))))))
...
...
@@ -90,7 +90,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testSingleUnzippedDbsnp
:
Unit
=
{
def
testSingleUnzippedDbsnp
()
:
Unit
=
{
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"
))))))
...
...
@@ -98,7 +98,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testMultiDbsnp
:
Unit
=
{
def
testMultiDbsnp
()
:
Unit
=
{
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"
))))))
...
...
@@ -106,7 +106,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testVep
:
Unit
=
{
def
testVep
()
:
Unit
=
{
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"
)))))
...
...
@@ -114,7 +114,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testGtfZipped
:
Unit
=
{
def
testGtfZipped
()
:
Unit
=
{
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"
)))))
...
...
@@ -122,7 +122,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testGtf
:
Unit
=
{
def
testGtf
()
:
Unit
=
{
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"
)))))
...
...
@@ -130,7 +130,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
}
@Test
def
testGff
:
Unit
=
{
def
testGff
()
:
Unit
=
{
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"
)))))
...
...
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