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biopet.biopet
Commits
7e6ef439
Commit
7e6ef439
authored
Sep 19, 2016
by
Peter van 't Hof
Browse files
Adding centrifuge to testing
parent
deced04c
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
7e6ef439
...
...
@@ -9,8 +9,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import
scala.util.matching.Regex
/**
* Created by pjvanthof on 19/09/16.
*/
* Created by pjvanthof on 19/09/16.
*/
class
Centrifuge
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
doc
=
"Input: FastQ or FastA"
,
required
=
true
)
var
inputR1
:
File
=
_
...
...
@@ -38,14 +38,14 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
def
versionRegex
:
Regex
=
".* version (.*)"
.
r
/**
* This function needs to be implemented to define the command that is executed
*
* @return Command to run
*/
* This function needs to be implemented to define the command that is executed
*
* @return Command to run
*/
def
cmdLine
:
String
=
executable
+
//TODO: Options
optional
(
"--threads"
,
threads
)
required
(
"-x"
,
index
)
+
required
(
"-x"
,
index
)
+
(
inputR2
match
{
case
Some
(
r2
)
=>
required
(
"-1"
,
inputR1
)
+
required
(
"-2"
,
r2
)
case
_
=>
required
(
"-U"
,
inputR1
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
7e6ef439
...
...
@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 19/09/16.
*/
* Created by pjvanthof on 19/09/16.
*/
class
CentrifugeKreport
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Output files centrifuge"
,
required
=
true
)
var
centrifugeOutputFiles
:
List
[
File
]
=
Nil
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
7e6ef439
...
...
@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 19/09/16.
*/
* Created by pjvanthof on 19/09/16.
*/
class
GearsCentrifuge
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
var
fastqR1
:
File
=
_
...
...
@@ -35,7 +35,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
add
(
centrifuge
)
val
centrifugeKreport
=
new
CentrifugeKreport
(
this
)
centrifugeKreport
.
centrifugeOutputFiles
+=
centrifuge
.
output
centrifugeKreport
.
centrifugeOutputFiles
:
+=
centrifuge
.
output
centrifugeKreport
.
output
=
new
File
(
outputDir
,
s
"$outputName.centrifuge.kreport"
)
add
(
centrifugeKreport
)
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
7e6ef439
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
...
...
@@ -49,6 +50,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
def
paired
:
Boolean
=
false
def
hasOutputName
:
Boolean
=
false
def
kraken
:
Option
[
Boolean
]
=
None
def
centrifuge
:
Boolean
=
false
def
qiimeClosed
:
Boolean
=
false
def
qiimeOpen
:
Boolean
=
false
def
qiimeRtax
:
Boolean
=
false
...
...
@@ -61,6 +63,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
def
testGears
()
:
Unit
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"gears_use_qiime_rtax"
->
qiimeRtax
,
"gears_use_centrifuge"
->
centrifuge
,
"gears_use_qiime_closed"
->
qiimeClosed
,
"gears_use_qiime_open"
->
qiimeOpen
,
"gears_use_seq_count"
->
seqCount
,
...
...
@@ -108,6 +111,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
summarySettings
(
"gear_use_qiime_open"
)
shouldBe
qiimeOpen
gears
.
krakenScript
.
isDefined
shouldBe
kraken
.
getOrElse
(
true
)
gears
.
centrifugeScript
.
isDefined
shouldBe
centrifuge
gears
.
qiimeClosed
.
isDefined
shouldBe
qiimeClosed
gears
.
qiimeOpen
.
isDefined
shouldBe
qiimeOpen
gears
.
qiimeRatx
.
isDefined
shouldBe
qiimeRtax
...
...
@@ -119,7 +123,11 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
(
if
(
kraken
.
getOrElse
(
true
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReport
])
shouldBe
(
if
(
kraken
.
getOrElse
(
true
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReportToJson
])
shouldBe
(
if
(
kraken
.
getOrElse
(
true
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReportToJson
])
shouldBe
((
if
(
kraken
.
getOrElse
(
true
))
1
else
0
)
+
(
if
(
centrifuge
)
1
else
0
))
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Centrifuge
])
shouldBe
(
if
(
centrifuge
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
CentrifugeKreport
])
shouldBe
(
if
(
centrifuge
)
1
else
0
)
}
}
}
...
...
@@ -132,6 +140,9 @@ class GearsSingleDefaultTest extends TestGearsSingle
class
GearsSingleKrakenTest
extends
TestGearsSingle
{
override
def
kraken
=
Some
(
true
)
}
class
GearsSingleCentrifugeTest
extends
TestGearsSingle
{
override
def
centrifuge
=
true
}
class
GearsSingleQiimeClosedTest
extends
TestGearsSingle
{
override
def
qiimeClosed
=
true
}
...
...
@@ -149,6 +160,10 @@ class GearsSingleKrakenPairedTest extends TestGearsSingle {
override
def
paired
=
true
override
def
kraken
=
Some
(
true
)
}
class
GearsSingleCentrifugePairedTest
extends
TestGearsSingle
{
override
def
paired
=
true
override
def
centrifuge
=
true
}
class
GearsSingleQiimeClosedPairedTest
extends
TestGearsSingle
{
override
def
paired
=
true
override
def
qiimeClosed
=
true
...
...
@@ -168,6 +183,7 @@ class GearsSingleseqCountPairedTest extends TestGearsSingle {
class
GearsSingleAllTest
extends
TestGearsSingle
{
override
def
kraken
=
Some
(
true
)
override
def
centrifuge
=
true
override
def
qiimeClosed
=
true
override
def
qiimeOpen
=
true
override
def
qiimeRtax
=
true
...
...
@@ -175,6 +191,7 @@ class GearsSingleAllTest extends TestGearsSingle {
}
class
GearsSingleAllPairedTest
extends
TestGearsSingle
{
override
def
kraken
=
Some
(
true
)
override
def
centrifuge
=
true
override
def
qiimeClosed
=
true
override
def
qiimeOpen
=
true
override
def
qiimeRtax
=
true
...
...
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