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biopet.biopet
Commits
97d82bfc
Commit
97d82bfc
authored
Jan 28, 2017
by
Peter van 't Hof
Browse files
Rename id to report
parent
ff41dff0
Changes
2
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala
View file @
97d82bfc
...
...
@@ -64,7 +64,7 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript
val
fastaFile
=
new
File
(
genomeDir
,
"reference.fa"
)
val
downloadFastaFile
=
new
File
(
genomeDir
,
"download.reference.fa"
)
genomeConfig
.
get
(
"ncbi_assembly_
id
"
)
match
{
genomeConfig
.
get
(
"ncbi_assembly_
report
"
)
match
{
case
Some
(
assemblyID
:
String
)
=>
val
downloadAssembly
=
new
DownloadNcbiAssembly
(
this
)
downloadAssembly
.
assemblyId
=
assemblyID
...
...
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @
97d82bfc
...
...
@@ -45,7 +45,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
@Test
def
testNcbiAssembly
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
Map
())
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"ncbi_assembly_
id
"
->
"id"
)))
pipeline
.
referenceConfig
=
Map
(
"s1"
->
Map
(
"g1"
->
Map
(
"ncbi_assembly_
report
"
->
"id"
)))
noException
should
be
thrownBy
pipeline
.
script
()
}
...
...
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