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biopet.biopet
Commits
98adc5f5
Commit
98adc5f5
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Fixed extensions in testing
parent
8054aa2d
Changes
2
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protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
98adc5f5
...
...
@@ -52,7 +52,7 @@ class ShivaTest extends TestNGSuite with Matchers {
var
m
:
Map
[
String
,
Any
]
=
ShivaTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample2
,
m
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test"
),
m
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test
.vcf.gz
"
),
m
)
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_variantcalling"
->
multi
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
)
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
98adc5f5
...
...
@@ -142,6 +142,6 @@ object ShivaVariantcallingTest {
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"input_alleles"
->
"test"
"input_alleles"
->
"test
.vcf.gz
"
)
}
\ No newline at end of file
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