Commit b8da950d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing code warning

parent 2b20899f
......@@ -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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