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biopet.biopet
Commits
a8a816b5
Commit
a8a816b5
authored
Jun 28, 2015
by
bow
Browse files
Style updates
parent
2db37a64
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
a8a816b5
...
...
@@ -95,7 +95,7 @@ class Gentrap(val root: Configurable) extends QScript
case
otherwise
=>
throw
new
IllegalStateException
(
otherwise
.
toString
)
}))
++
(
ribosomalRefFlat
match
{
case
Some
(
rbs
)
=>
Map
(
"ribosomal_intervals"
->
rbs
.
toString
)
case
None
=>
Map
()
case
None
=>
Map
()
})
/** Default pipeline config */
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a8a816b5
...
...
@@ -377,7 +377,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
sorter
.
sortOrder
=
"coordinate"
sorter
.
isIntermediate
=
true
add
(
sorter
)
// merge with mapped file
val
mergeSamFile
=
MergeSamFiles
(
this
,
List
(
tophat
.
outputAcceptedHits
,
sorter
.
output
),
tophat
.
output_dir
,
"coordinate"
)
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
View file @
a8a816b5
...
...
@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the tophat-recondition.py script.
*
*
* NOTE: we are modifying the input and output to be the BAM files directly so the wrapper works nice with Queue.
*/
class
TophatRecondition
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
@@ -45,6 +45,6 @@ class TophatRecondition(val root: Configurable) extends PythonCommandLineFunctio
require
(
inputBam
!=
null
,
"Input must be defined."
)
require
(
outputSam
!=
null
,
"Output must be defined."
)
}
def
cmdLine
=
getPythonCommand
+
required
(
inputDir
)
+
required
(
outputDir
)
}
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