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biopet.biopet
Commits
6f754064
Commit
6f754064
authored
Jun 07, 2016
by
Peter van 't Hof
Browse files
Added to generateIndexes
parent
40802e4e
Changes
3
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
View file @
6f754064
...
...
@@ -42,9 +42,8 @@ class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with
var
localftabchars
:
Option
[
Int
]
=
config
(
"localftabchars"
)
var
seed
:
Option
[
Int
]
=
config
(
"seed"
)
var
large
-
index
:
Boolean
=
config
(
"large-index"
,
default
=
false
)
var
dcv
:
Boolean
=
config
(
"dcv"
,
default
=
false
)
var
memory
-
fitting
:
Boolean
=
config
(
"memory-fitting"
,
default
=
false
)
var
largeIndex
:
Boolean
=
config
(
"large_index"
,
default
=
false
)
var
memoryFitting
:
Boolean
=
config
(
"memory_fitting"
,
default
=
false
)
var
nodc
:
Boolean
=
config
(
"nodc"
,
default
=
false
)
var
noref
:
Boolean
=
config
(
"noref"
,
default
=
false
)
var
justref
:
Boolean
=
config
(
"justref"
,
default
=
false
)
...
...
@@ -70,9 +69,8 @@ class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with
optional
(
"--haplotype"
,
haplotype
)
+
optional
(
"--ss"
,
ss
)
+
optional
(
"--exon"
,
exon
)
+
conditional
(
large
-
index
,
"--large-index"
)
+
conditional
(
dcv
,
"--dcv"
)
+
conditional
(
memory
-
fitting
,
"--memory-fitting"
)
+
conditional
(
largeIndex
,
"--large-index"
)
+
conditional
(
memoryFitting
,
"--memory-fitting"
)
+
conditional
(
nodc
,
"--nodc"
)
+
conditional
(
noref
,
"--noref"
)
+
conditional
(
justref
,
"--justref"
)
+
...
...
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
View file @
6f754064
...
...
@@ -14,16 +14,17 @@
*/
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
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2Build
import
nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
import
nl.lumc.sasc.biopet.utils.ConfigUtils
...
...
@@ -267,6 +268,17 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
"bowtie_index"
->
bowtie2Index
.
reference
.
getAbsolutePath
.
stripSuffix
(
".fa"
).
stripSuffix
(
".fasta"
)
)
// Hisat2 index
val
hisat2Index
=
new
Hisat2Build
(
this
)
hisat2Index
.
inputFasta
=
createLinks
(
new
File
(
genomeDir
,
"hisat2"
))
hisat2Index
.
hisat2IndexBase
=
new
File
(
new
File
(
genomeDir
,
"hisat2"
),
"reference"
).
getAbsolutePath
add
(
hisat2Index
)
configDeps
:+=
hisat2Index
.
jobOutputFile
outputConfig
+=
"hisat2"
->
Map
(
"reference_fasta"
->
hisat2Index
.
inputFasta
.
getAbsolutePath
,
"hisat_index"
->
hisat2Index
.
inputFasta
.
getAbsolutePath
.
stripSuffix
(
".fa"
).
stripSuffix
(
".fasta"
)
)
val
writeConfig
=
new
WriteConfig
writeConfig
.
deps
=
configDeps
writeConfig
.
out
=
new
File
(
genomeDir
,
s
"$speciesName-$genomeName.json"
)
...
...
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexesTest.scala
View file @
6f754064
...
...
@@ -102,6 +102,7 @@ object GenerateIndexesTest {
val
config
=
Map
(
"output_dir"
->
outputDir
,
"bwa"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"hisat2build"
->
Map
(
"exe"
->
"test"
),
"bowtiebuild"
->
Map
(
"exe"
->
"test"
),
"bowtie2build"
->
Map
(
"exe"
->
"test"
),
"gmapbuild"
->
Map
(
"exe"
->
"test"
),
...
...
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