Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
50382ca3
Commit
50382ca3
authored
Nov 29, 2016
by
Peter van 't Hof
Browse files
Fixinf nullpointers on unit tests
parent
7336a86d
Changes
21
Hide whitespace changes
Inline
Side-by-side
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
),
...
...
Prev
1
2
Next
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment