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biopet.biopet
Commits
50382ca3
Commit
50382ca3
authored
Nov 29, 2016
by
Peter van 't Hof
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Fixinf nullpointers on unit tests
parent
7336a86d
Changes
21
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21 changed files
with
29 additions
and
3 deletions
+29
-3
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+1
-0
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
+1
-0
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+3
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+5
-1
carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+1
-0
flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+1
-0
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
...nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+1
-0
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+1
-0
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
...iopet/pipelines/generateindexes/DownloadGenomesTest.scala
+3
-1
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+1
-0
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
...nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
+1
-0
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
+1
-0
kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
+1
-0
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+1
-0
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
+1
-0
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
+1
-0
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+1
-0
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+1
-0
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+1
-0
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+1
-0
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+1
-0
No files found.
bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
50382ca3
...
...
@@ -114,6 +114,7 @@ object BamMetricsTest {
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"refFlat"
->
"bla.refFlat"
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
50382ca3
...
...
@@ -144,6 +144,7 @@ object BastyTest {
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"cache"
->
true
,
"dir"
->
"test"
,
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
50382ca3
...
...
@@ -63,6 +63,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
/** Returns the extension to make the report */
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
None
val
skipWriteDependencies
:
Boolean
=
config
(
"skip_write_dependencies"
,
default
=
false
)
/** Script from queue itself, final to force some checks for each pipeline and write report */
final
def
script
()
{
outputDir
=
config
(
"output_dir"
)
...
...
@@ -122,7 +124,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
".log"
),
qSettings
.
runName
)
if
(!
skipWriteDependencies
)
WriteDependencies
.
writeDependencies
(
functions
,
new
File
(
outputDir
,
".log"
),
qSettings
.
runName
)
Logging
.
checkErrors
()
logger
.
info
(
"Script complete without errors"
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
50382ca3
...
...
@@ -57,7 +57,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
for
(
q
<-
qscript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
qscript
.
summarizables
;
s
<-
l
)
s
match
{
case
f
:
QFunction
=>
deps
:+=
f
.
firstOutput
case
f
:
QFunction
=>
try
{
deps
:+=
f
.
firstOutput
}
catch
{
case
e
:
NullPointerException
=>
logger
.
warn
(
"Queue values are not init"
)
}
case
_
=>
}
...
...
carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
50382ca3
...
...
@@ -117,6 +117,7 @@ object CarpTest {
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
...
...
flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
50382ca3
...
...
@@ -115,6 +115,7 @@ object FlexiprepTest {
Files
.
touch
(
r2Zipped
)
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"seqstat"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
50382ca3
...
...
@@ -234,6 +234,7 @@ object TestGearsSingle {
bam
.
deleteOnExit
()
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"centrifuge"
->
Map
(
"exe"
->
"test"
,
"centrifuge_index"
->
"test"
),
"centrifugekreport"
->
Map
(
"exe"
->
"test"
),
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @
50382ca3
...
...
@@ -113,6 +113,7 @@ object GearsTest {
Files
.
touch
(
bam
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"output_dir"
->
outputDir
,
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
...
...
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @
50382ca3
...
...
@@ -141,7 +141,9 @@ object DownloadGenomesTest {
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
val
config
=
Map
(
"output_dir"
->
outputDir
,
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"output_dir"
->
outputDir
,
"bwa"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"hisat2build"
->
Map
(
"exe"
->
"test"
),
...
...
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
50382ca3
...
...
@@ -186,6 +186,7 @@ object GentrapTest {
copyFile
(
"ref.fa.fai"
)
val
executables
:
Map
[
String
,
Any
]
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"refFlat"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"annotation_gtf"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
...
...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
View file @
50382ca3
...
...
@@ -75,6 +75,7 @@ object GwasTestTest {
}
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
reference
.
toString
,
"phenotype_file"
->
phenotypeFile
.
toString
,
"output_dir"
->
outputDir
,
...
...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
View file @
50382ca3
...
...
@@ -93,6 +93,7 @@ object Impute2VcfTest {
}
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
reference
.
toString
,
"phenotype_file"
->
phenotypeFile
.
toString
,
"output_dir"
->
outputDir
,
...
...
kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
View file @
50382ca3
...
...
@@ -112,6 +112,7 @@ object KopisuTest {
Files
.
touch
(
new
File
(
controlDir
,
"test.txt"
))
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
50382ca3
...
...
@@ -128,6 +128,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
}
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"db"
->
"test"
,
"bowtie_index"
->
(
outputDir
+
File
.
separator
+
"ref"
),
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
50382ca3
...
...
@@ -184,6 +184,7 @@ object MultisampleMappingTestTrait {
copyFile
(
"empty.sam"
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"cache"
->
true
,
"dir"
->
"test"
,
...
...
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
View file @
50382ca3
...
...
@@ -131,6 +131,7 @@ object SageTest {
copyFile
(
"ref.fa.fai"
)
val
config
:
Map
[
String
,
Any
]
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"output_dir"
->
outputDir
.
getAbsolutePath
,
"fastqc"
->
Map
(
"exe"
->
"test"
),
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
50382ca3
...
...
@@ -198,6 +198,7 @@ object ShivaSvCallingTest {
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"cache"
->
true
,
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
50382ca3
...
...
@@ -191,6 +191,7 @@ object ShivaTest {
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"cache"
->
true
,
"dir"
->
"test"
,
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
50382ca3
...
...
@@ -230,6 +230,7 @@ object ShivaVariantcallingTest {
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"cache"
->
true
,
...
...
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
View file @
50382ca3
...
...
@@ -119,6 +119,7 @@ object TinyCapTest {
Files
.
touch
(
annotationRefflat
)
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"output_dir"
->
outputDir
,
"reference_fasta"
->
(
referenceFasta
.
getAbsolutePath
),
"bowtie_index"
->
(
bowtieIndex
.
getAbsolutePath
),
...
...
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
View file @
50382ca3
...
...
@@ -107,6 +107,7 @@ object ToucanTest {
exacVcfFile
.
deleteOnExit
()
val
config
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
resourcePath
(
"/fake_chrQ.fa"
),
"output_dir"
->
outputDir
,
"gatk_jar"
->
"test"
,
...
...
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