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biopet.biopet
Commits
b5c6727b
Commit
b5c6727b
authored
Dec 29, 2015
by
Peter van 't Hof
Browse files
Moved flash as general job
parent
1cdd1970
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
View file @
b5c6727b
...
...
@@ -19,9 +19,7 @@ import scala.xml.{ PrettyPrinter, Elem }
*/
class
GearsQiimeClosed
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
var
fastqR1
:
File
=
_
var
fastqR2
:
Option
[
File
]
=
None
var
fastqInput
:
File
=
_
override
def
defaults
=
Map
(
"splitlibrariesfastq"
->
Map
(
...
...
@@ -30,7 +28,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
)
def
init
()
=
{
require
(
fastq
R1
!=
null
)
require
(
fastq
Input
!=
null
)
}
private
var
_otuMap
:
File
=
_
...
...
@@ -41,19 +39,8 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
def
biopetScript
()
=
{
val
fastqFile
=
fastqR2
match
{
case
Some
(
r2
)
=>
val
flash
=
new
Flash
(
this
)
flash
.
outputDirectory
=
new
File
(
outputDir
,
"combine_reads_flash"
)
flash
.
fastqR1
=
fastqR1
flash
.
fastqR2
=
r2
add
(
flash
)
flash
.
combinedFastq
case
_
=>
fastqR1
}
val
splitLib
=
new
SplitLibrariesFastq
(
this
)
splitLib
.
input
:+=
fastq
File
splitLib
.
input
:+=
fastq
Input
splitLib
.
outputDir
=
new
File
(
outputDir
,
"split_libraries_fastq"
)
sampleId
.
foreach
(
splitLib
.
sample_ids
:+=
_
)
add
(
splitLib
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
b5c6727b
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.Flash
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -100,6 +101,19 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case
_
=>
throw
new
IllegalArgumentException
(
"Missing input files"
)
}
lazy
val
combinedFastq
=
{
r2
match
{
case
Some
(
r2
)
=>
val
flash
=
new
Flash
(
this
)
flash
.
outputDirectory
=
new
File
(
outputDir
,
"combine_reads_flash"
)
flash
.
fastqR1
=
r1
flash
.
fastqR2
=
r2
add
(
flash
)
flash
.
combinedFastq
case
_
=>
r1
}
}
krakenScript
foreach
{
kraken
=>
kraken
.
outputDir
=
new
File
(
outputDir
,
"kraken"
)
kraken
.
fastqR1
=
r1
...
...
@@ -117,8 +131,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeClosed
foreach
{
qiimeClosed
=>
qiimeClosed
.
outputDir
=
new
File
(
outputDir
,
"qiime_closed"
)
qiimeClosed
.
fastqR1
=
r1
qiimeClosed
.
fastqR2
=
r2
qiimeClosed
.
fastqInput
=
combinedFastq
add
(
qiimeClosed
)
//TODO: Plots
...
...
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