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biopet.biopet
Commits
caf77b81
Commit
caf77b81
authored
Oct 19, 2015
by
Wai Yi Leung
Browse files
Style update by IDEA
parent
d82b56a0
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
View file @
caf77b81
...
...
@@ -32,9 +32,9 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
override
def
defaultCoreMemory
=
1.0
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-i"
,
inputReport
)
+
required
(
"-o"
,
output
)
+
conditional
(
skipNames
,
"--skipnames"
)
required
(
"-i"
,
inputReport
)
+
required
(
"-o"
,
output
)
+
conditional
(
skipNames
,
"--skipnames"
)
def
summaryStats
:
Map
[
String
,
Any
]
=
{
val
map
=
ConfigUtils
.
fileToConfigMap
(
output
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
caf77b81
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
SortSam
,
SamToFastq
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
SortSam
,
SamToFastq
}
import
nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import
nl.lumc.sasc.biopet.extensions.tools.
{
KrakenReportToJson
,
FastqSync
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -76,7 +76,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
// start bam to fastq (only on unaligned reads) also extract the matesam
val
samToFastq
=
new
SamToFastq
(
qscript
)
samToFastq
.
input
=
samFilterUnmapped
.
output
samToFastq
.
input
=
samFilterUnmapped
.
output
samToFastq
.
stringency
=
Some
(
"LENIENT"
)
samToFastq
.
fastqR1
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R1.fq.gz"
)
samToFastq
.
fastqR2
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.fq.gz"
)
...
...
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