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biopet.biopet
Commits
ec99ed54
Commit
ec99ed54
authored
Jun 07, 2016
by
Peter van 't Hof
Browse files
Added mapping tests for hisat2
parent
6f754064
Changes
4
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
View file @
ec99ed54
...
...
@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.hisat
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 7-6-16.
*/
* Created by pjvan_thof on 7-6-16.
*/
class
Hisat2Build
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
...
...
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
View file @
ec99ed54
...
...
@@ -14,13 +14,13 @@
*/
package
nl.lumc.sasc.biopet.pipelines.generateindexes
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
java.util
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2Build
,
BowtieBuild
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2Build
,
BowtieBuild
}
import
nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
...
...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
View file @
ec99ed54
...
...
@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 31-5-16.
*/
* Created by pjvan_thof on 31-5-16.
*/
class
Impute2VcfTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Impute2Vcf
=
{
new
Impute2Vcf
{
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
ec99ed54
...
...
@@ -98,6 +98,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
val
r2
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq"
)
val
r1Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
val
r2Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq.gz"
)
val
hisat2Index
=
new
File
(
outputDir
,
"ref.1.ht2"
)
@BeforeClass
def
createTempFiles
:
Unit
=
{
...
...
@@ -105,6 +106,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
Files
.
touch
(
r2
)
Files
.
touch
(
r1Zipped
)
Files
.
touch
(
r2Zipped
)
Files
.
touch
(
hisat2Index
)
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
...
...
@@ -125,6 +127,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"db"
->
"test"
,
"bowtie_index"
->
(
outputDir
+
File
.
separator
+
"ref"
),
"hisat2_index"
->
(
outputDir
+
File
.
separator
+
"ref"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"gsnap"
->
Map
(
"exe"
->
"test"
),
...
...
@@ -135,6 +138,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
"star"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"bowtie2"
->
Map
(
"exe"
->
"test"
),
"hisat2"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
,
"genome"
->
"test"
,
"hash"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
...
...
@@ -154,6 +158,7 @@ class MappingStarTest extends AbstractTestMapping("star")
class
MappingStar2PassTest
extends
AbstractTestMapping
(
"star-2pass"
)
class
MappingBowtieTest
extends
AbstractTestMapping
(
"bowtie"
)
class
MappingBowtie2Test
extends
AbstractTestMapping
(
"bowtie2"
)
class
MappingHisat2Test
extends
AbstractTestMapping
(
"hisat2"
)
class
MappingStampyTest
extends
AbstractTestMapping
(
"stampy"
)
class
MappingGsnapTest
extends
AbstractTestMapping
(
"gsnap"
)
class
MappingTophatTest
extends
AbstractTestMapping
(
"tophat"
)
...
...
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