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biopet.biopet
Commits
43100197
Commit
43100197
authored
Dec 17, 2015
by
Peter van 't Hof
Browse files
Style fixes
parent
08070144
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
43100197
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Zcat
,
Ln
}
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Zcat
,
Ln
}
import
nl.lumc.sasc.biopet.extensions.qiime.
{
MergeOtuMaps
,
MergeOtuTables
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -127,10 +127,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
val
mergeR1
:
File
=
new
File
(
sampleDir
,
s
"$sampleId.R1.fq.gz"
)
add
(
Zcat
(
qscript
,
flexipreps
.
map
(
_
.
fastqR1Qc
))
|
new
Gzip
(
qscript
)
>
mergeR1
)
val
mergeR2
=
if
(
flexipreps
.
exists
(
_
.
paired
))
{
Some
(
new
File
(
sampleDir
,
s
"$sampleId.R2.fq.gz"
))
}
else
None
val
mergeR2
=
if
(
flexipreps
.
exists
(
_
.
paired
))
Some
(
new
File
(
sampleDir
,
s
"$sampleId.R2.fq.gz"
))
else
None
mergeR2
.
foreach
{
file
=>
add
(
Zcat
(
qscript
,
flexipreps
.
flatMap
(
_
.
fastqR2Qc
))
|
new
Gzip
(
qscript
)
>
file
)
}
...
...
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