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biopet.biopet
Commits
75ee4ec8
Commit
75ee4ec8
authored
Mar 01, 2016
by
Wai Yi Leung
Browse files
Adding tests to Flexiprep to cover the FastQ validation and abort on corrupt FastQ
parent
36b0881c
Changes
1
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public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
75ee4ec8
...
...
@@ -18,10 +18,9 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Sickle
,
Zcat
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
SeqStat
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
ValidateFastq
,
SeqStat
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
...
...
@@ -50,20 +49,24 @@ class FlexiprepTest extends TestNGSuite with Matchers {
val
skipTrims
=
Array
(
true
,
false
)
val
skipClips
=
Array
(
true
,
false
)
val
zipped
=
Array
(
true
,
false
)
val
abortOnCorruptFastqs
=
Array
(
true
,
false
)
for
(
pair
<-
paired
;
skipTrim
<-
skipTrims
;
skipClip
<-
skipClips
;
zip
<-
zipped
)
yield
Array
(
""
,
pair
,
skipTrim
,
skipClip
,
zip
)
zip
<-
zipped
;
abortOnCorruptFastq
<-
abortOnCorruptFastqs
)
yield
Array
(
""
,
pair
,
skipTrim
,
skipClip
,
zip
,
abortOnCorruptFastq
)
}
@Test
(
dataProvider
=
"flexiprepOptions"
)
def
testFlexiprep
(
f
:
String
,
paired
:
Boolean
,
skipTrim
:
Boolean
,
skipClip
:
Boolean
,
zipped
:
Boolean
)
=
{
def
testFlexiprep
(
f
:
String
,
paired
:
Boolean
,
skipTrim
:
Boolean
,
skipClip
:
Boolean
,
zipped
:
Boolean
,
abortOnCorruptFastq
:
Boolean
)
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
FlexiprepTest
.
outputDir
,
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
"skip_clip"
->
skipClip
,
"abort_on_corrupt_fastq"
->
abortOnCorruptFastq
),
Map
(
FlexiprepTest
.
executables
.
toSeq
:
_
*
))
val
flexiprep
:
Flexiprep
=
initPipeline
(
map
)
...
...
@@ -75,6 +78,10 @@ class FlexiprepTest extends TestNGSuite with Matchers {
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Fastqc
])
shouldBe
(
if
(
paired
)
4
else
2
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
SeqStat
])
shouldBe
(
if
(
paired
)
4
else
2
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
ValidateFastq
])
shouldBe
2
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
CheckValidateFastq
])
shouldBe
(
if
(
abortOnCorruptFastq
)
2
else
0
)
}
// remove temporary run directory all tests in the class have been run
...
...
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