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biopet.biopet
Commits
f66115cc
Commit
f66115cc
authored
Aug 22, 2014
by
Peter van 't Hof
Browse files
Convert SortSam to biopet function
parent
2cd4fb00
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
0 → 100644
View file @
f66115cc
package
nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
class
SortSam
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"picard.sam.SortSam"
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
File
=
_
@Output
(
doc
=
"The output file to bam file to"
,
required
=
true
)
var
output
:
File
=
_
@Argument
(
doc
=
"Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} "
,
required
=
true
)
var
sortOrder
:
String
=
_
override
def
commandLine
=
super
.
commandLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
required
(
"SORT_ORDER="
,
sortOrder
,
spaceSeparated
=
false
)
}
object
SortSam
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
,
sortOrder
:
String
=
null
)
:
SortSam
=
{
val
sortSam
=
new
SortSam
(
root
)
sortSam
.
input
=
input
sortSam
.
output
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
).
stripSuffix
(
".sam"
)
+
".sorted.bam"
)
if
(
sortOrder
==
null
)
sortSam
.
sortOrder
=
"coordinate"
else
sortSam
.
sortOrder
=
sortOrder
return
sortSam
}
}
\ No newline at end of file
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
f66115cc
...
...
@@ -6,12 +6,12 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.apps.FastqSplitter
import
nl.lumc.sasc.biopet.extensions.aligners.
{
Bwa
,
Star
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
,
ClassType
}
import
org.broadinstitute.gatk.queue.extensions.picard.
{
MergeSamFiles
,
SortSam
,
AddOrReplaceReadGroups
}
import
org.broadinstitute.gatk.queue.extensions.picard.
{
MergeSamFiles
,
AddOrReplaceReadGroups
}
import
scala.math._
class
Mapping
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
@@ -192,7 +192,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaCommand
.
R
=
getReadGroup
bwaCommand
.
output
=
new
File
(
chunkDir
+
outputName
+
".sam"
)
add
(
bwaCommand
,
isIntermediate
=
true
)
bamFiles
:+=
addSortSam
(
List
(
bwaCommand
.
output
),
swapExt
(
chunkDir
,
bwaCommand
.
output
,
".sam"
,
".bam"
),
chunkDir
)
val
sortSam
=
SortSam
(
this
,
bwaCommand
.
output
,
chunkDir
)
if
(
chunking
||
!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
add
(
sortSam
)
bamFiles
:+=
sortSam
.
output
}
else
if
(
aligner
==
"star"
)
{
val
starCommand
=
Star
(
this
,
R1
,
if
(
paired
)
R2
else
null
,
outputDir
,
isIntermediate
=
true
,
deps
=
deps
)
add
(
starCommand
)
...
...
@@ -219,19 +222,19 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
outputFiles
+=
(
"finalBamFile"
->
bamFile
)
}
def
addSortSam
(
inputSam
:
List
[
File
],
outputFile
:
File
,
dir
:
String
)
:
File
=
{
val
sortSam
=
new
SortSam
sortSam
.
input
=
inputSam
sortSam
.
createIndex
=
true
sortSam
.
output
=
outputFile
sortSam
.
memoryLimit
=
2
sortSam
.
nCoresRequest
=
2
sortSam
.
jobResourceRequests
:+=
"h_vmem=4G"
if
(!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
add
(
sortSam
)
return
sortSam
.
output
}
//
def addSortSam(inputSam: List[File], outputFile: File, dir: String): File = {
//
val sortSam = new SortSam
//
sortSam.input = inputSam
//
sortSam.createIndex = true
//
sortSam.output = outputFile
//
sortSam.memoryLimit = 2
//
sortSam.nCoresRequest = 2
//
sortSam.jobResourceRequests :+= "h_vmem=4G"
//
if (!skipMarkduplicates) sortSam.isIntermediate = true
//
add(sortSam)
//
//
return sortSam.output
//
}
def
addMergeBam
(
inputSam
:
List
[
File
],
outputFile
:
File
,
dir
:
String
)
:
File
=
{
val
mergeSam
=
new
MergeSamFiles
...
...
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