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biopet.biopet
Commits
2cc410f4
Commit
2cc410f4
authored
Mar 01, 2017
by
Peter van 't Hof
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Adding separated outputDirs for tests
parent
407c69a0
Changes
2
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2 changed files
with
19 additions
and
12 deletions
+19
-12
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+18
-11
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+1
-1
No files found.
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
2cc410f4
...
...
@@ -95,14 +95,20 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
pipesJobs
.
count
(
_
.
isInstanceOf
[
Centrifuge
])
shouldBe
(
if
(
unmappedToGears
)
1
else
0
)
}
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
private
var
dirs
:
List
[
File
]
=
Nil
def
outputDir
:
File
=
{
val
dir
=
Files
.
createTempDir
()
dirs
:+=
dir
dir
}
val
inputDir
=
Files
.
createTempDir
()
val
r1
=
new
File
(
out
putDir
,
"input"
+
File
.
separator
+
"R1.fq"
)
val
r2
=
new
File
(
out
putDir
,
"input"
+
File
.
separator
+
"R2.fq"
)
val
r1Zipped
=
new
File
(
out
putDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
val
r2Zipped
=
new
File
(
out
putDir
,
"input"
+
File
.
separator
+
"R2.fq.gz"
)
val
hisat2Index
=
new
File
(
out
putDir
,
"ref.1.ht2"
)
val
r1
=
new
File
(
in
putDir
,
"input"
+
File
.
separator
+
"R1.fq"
)
val
r2
=
new
File
(
in
putDir
,
"input"
+
File
.
separator
+
"R2.fq"
)
val
r1Zipped
=
new
File
(
in
putDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
val
r2Zipped
=
new
File
(
in
putDir
,
"input"
+
File
.
separator
+
"R2.fq.gz"
)
val
hisat2Index
=
new
File
(
in
putDir
,
"ref.1.ht2"
)
@BeforeClass
def
createTempFiles
:
Unit
=
{
...
...
@@ -129,10 +135,10 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
val
executables
=
Map
(
"skip_write_dependencies"
->
true
,
"reference_fasta"
->
(
out
putDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
in
putDir
+
File
.
separator
+
"ref.fa"
),
"db"
->
"test"
,
"bowtie_index"
->
(
out
putDir
+
File
.
separator
+
"ref"
),
"hisat2_index"
->
(
out
putDir
+
File
.
separator
+
"ref"
),
"bowtie_index"
->
(
in
putDir
+
File
.
separator
+
"ref"
),
"hisat2_index"
->
(
in
putDir
+
File
.
separator
+
"ref"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"gsnap"
->
Map
(
"exe"
->
"test"
),
...
...
@@ -156,7 +162,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
outputDir
)
FileUtils
.
deleteDirectory
(
inputDir
)
dirs
.
foreach
(
FileUtils
.
deleteDirectory
)
}
}
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
2cc410f4
...
...
@@ -106,7 +106,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
/** Files page, can be used general or at sample level */
override
def
filesPage
(
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
ReportPage
=
{
val
vcfFilesSection
=
if
(
variantcallingExecuted
)
List
(
"VCF files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp"
,
Map
(
"sampleId"
->
None
)))
Map
(
"sampleId"
->
sampleId
)))
else
Nil
val
oldPage
=
super
.
filesPage
(
sampleId
,
libraryId
)
oldPage
.
copy
(
sections
=
oldPage
.
sections
++
vcfFilesSection
)
...
...
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