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biopet.biopet
Commits
86e7d090
Commit
86e7d090
authored
Dec 18, 2015
by
Peter van 't Hof
Browse files
Add settings
parent
8acebe9a
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
86e7d090
...
...
@@ -73,8 +73,10 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
Some
(
gears
)
}
protected
var
skipFlexiprep
:
Boolean
=
config
(
"skip_flexiprep"
,
default
=
false
)
protected
def
executeFlexiprep
(
r1
:
File
,
r2
:
Option
[
File
])
:
(
File
,
Option
[
File
])
=
{
if
(!
config
(
"
skip
_f
lexiprep
"
,
default
=
false
).
asBoolean
)
{
if
(!
skip
F
lexiprep
)
{
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
input_R1
=
r1
flexiprep
.
input_R2
=
r2
...
...
@@ -129,7 +131,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".gears.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
.
empty
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"skip_flexiprep"
->
skipFlexiprep
,
"gears_use_kraken"
->
krakenScript
.
isDefined
,
"gear_use_qiime_rtax"
->
qiimeRatx
.
isDefined
,
"gear_use_qiime_closed"
->
qiimeClosed
.
isDefined
)
/** Statistics shown in the summary file */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
.
empty
++
...
...
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