Commit 2b20899f authored by Peter van 't Hof's avatar Peter van 't Hof

Fix style

parent d24adc45
......@@ -69,7 +69,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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")))))
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz")))))
pipeline.script()
}
......@@ -77,7 +77,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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"))))))
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz", "contig_map" -> Map("1" -> "chr1"))))))
pipeline.script()
}
......@@ -85,7 +85,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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"))))))
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf", "contig_map" -> Map("1" -> "chr1"))))))
pipeline.script()
}
......@@ -93,7 +93,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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"))))))
"dbsnp" -> Map("version" -> Map(("vcf_uri" -> "uri.vcf"))))))
pipeline.script()
}
......@@ -101,7 +101,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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"))))))
"dbsnp" -> Map("version" -> Map("vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))))
pipeline.script()
}
......@@ -109,7 +109,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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")))))
"vep" -> Map("version" -> Map("cache_uri" -> "something/human_vep_80_hg19.tar.gz")))))
pipeline.script()
}
......@@ -117,7 +117,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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")))))
"gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf.gz")))))
pipeline.script()
}
......@@ -125,7 +125,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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")))))
"gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf")))))
pipeline.script()
}
......@@ -133,7 +133,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
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")))))
"gene_annotation" -> Map("version" -> Map("gff_uri" -> "bla.gf")))))
pipeline.script()
}
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment