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biopet.biopet
Commits
bc930d51
Commit
bc930d51
authored
Jan 25, 2017
by
Peter van 't Hof
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Make centrifuge usable output method
parent
d36878da
Changes
1
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1 changed file
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13 additions
and
10 deletions
+13
-10
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+13
-10
No files found.
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
bc930d51
...
...
@@ -94,18 +94,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
Some
(
outputFile
)
}
if
(!
skipFlexiprep
)
{
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
inputR1
=
read1
flexiprep
.
inputR2
=
read2
flexiprep
.
sampleId
=
if
(
sampleId
.
isEmpty
)
Some
(
"noSampleName"
)
else
sampleId
flexiprep
.
libId
=
if
(
libId
.
isEmpty
)
Some
(
"noLibName"
)
else
libId
flexiprep
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
add
(
flexiprep
)
(
flexiprep
.
fastqR1Qc
,
flexiprep
.
fastqR2Qc
)
}
else
(
read1
,
read2
)
flexiprep
.
map
{
f
=>
f
.
inputR1
=
read1
f
.
inputR2
=
read2
f
.
sampleId
=
Some
(
sampleId
.
getOrElse
(
"noSampleName"
))
f
.
libId
=
Some
(
libId
.
getOrElse
(
"noLibName"
))
f
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
add
(
f
)
(
f
.
fastqR1Qc
,
f
.
fastqR2Qc
)
}.
getOrElse
((
read1
,
read2
))
}
lazy
protected
val
flexiprep
:
Option
[
Flexiprep
]
=
if
(!
skipFlexiprep
)
{
Some
(
new
Flexiprep
(
this
))
}
else
None
/** Method to add jobs */
def
biopetScript
()
:
Unit
=
{
val
(
r1
,
r2
)
:
(
File
,
Option
[
File
])
=
(
fastqR1
,
fastqR2
,
bamFile
)
match
{
...
...
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