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biopet.biopet
Commits
52928227
Commit
52928227
authored
Oct 02, 2015
by
Peter van 't Hof
Browse files
Fix code style warnings
parent
699c7baf
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
52928227
...
...
@@ -15,11 +15,9 @@
*/
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.
{
Pbzip2
,
Zcat
,
Gzip
,
Sickle
}
import
nl.lumc.sasc.biopet.extensions.
{
Zcat
,
Gzip
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.tools.
{
SeqStat
,
FastqSync
}
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -109,7 +107,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def
biopetScript
()
{
runInitialJobs
()
val
out
=
if
(
paired
)
runTrimClip
(
input_R1
,
input_R2
,
outputDir
)
if
(
paired
)
runTrimClip
(
input_R1
,
input_R2
,
outputDir
)
else
runTrimClip
(
input_R1
,
outputDir
)
val
R1_files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R1"
))
yield
v
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
52928227
...
...
@@ -19,7 +19,6 @@ import java.io.File
import
java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsSort
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
...
...
@@ -178,13 +177,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
var
fastq_R2_output
:
List
[
File
]
=
Nil
val
chunks
:
Map
[
File
,
(
File
,
Option
[
File
])]
=
{
if
(
chunking
)
{
(
for
(
t
<-
1
to
numberChunks
.
getOrElse
(
1
))
yield
{
val
chunkDir
=
new
File
(
outputDir
,
"chunks"
+
File
.
separator
+
t
)
chunkDir
->
(
new
File
(
chunkDir
,
input_R1
.
getName
),
if
(
paired
)
Some
(
new
File
(
chunkDir
,
input_R2
.
get
.
getName
))
else
None
)
}).
toMap
}
else
if
(
skipFlexiprep
)
Map
(
outputDir
->
(
input_R1
,
(
if
(
paired
)
input_R2
else
None
)))
if
(
chunking
)
(
for
(
t
<-
1
to
numberChunks
.
getOrElse
(
1
))
yield
{
val
chunkDir
=
new
File
(
outputDir
,
"chunks"
+
File
.
separator
+
t
)
chunkDir
->
(
new
File
(
chunkDir
,
input_R1
.
getName
),
if
(
paired
)
Some
(
new
File
(
chunkDir
,
input_R2
.
get
.
getName
))
else
None
)
}).
toMap
else
if
(
skipFlexiprep
)
Map
(
outputDir
->
(
input_R1
,
if
(
paired
)
input_R2
else
None
))
else
Map
(
outputDir
->
(
flexiprep
.
input_R1
,
flexiprep
.
input_R2
))
}
...
...
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