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biopet.biopet
Commits
cf8259b9
Commit
cf8259b9
authored
Jul 24, 2017
by
Ruben Vorderman
Browse files
Removed some variables from ssp file.
parent
e859f656
Changes
2
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Inline
Side-by-side
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
cf8259b9
...
...
@@ -33,6 +33,8 @@
<%@ var librariesCount: Int %>
<%@ var clipCount: Int %>
<%@ var trimCount: Int %>
<%@ var flexiprepReportPlotRead1: Option[Unit] %>
<%@ var flexiprepReportPlotRead2: Option[Unit] %>
<%@ var %>
#if (showIntro)
...
...
@@ -76,8 +78,8 @@
#if (showPlot)
#{
F
lexiprepReport
.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId
)
if (paired)
F
lexiprepReport
.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId
)
f
lexiprepReport
PlotRead1.getOrElse(None
)
if (paired)
f
lexiprepReport
PlotRead2.getOrElse(None
)
}#
<div class="panel-body">
<div class="row">
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
cf8259b9
...
...
@@ -296,11 +296,13 @@ object FlexiprepReadSummary {
object
FlexiprepReadSummaryReportPage
{
def
values
(
summary
:
SummaryDb
,
outputDir
:
File
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
]
=
None
,
libId
:
Option
[
Int
]
=
None
)
=
{
libId
:
Option
[
Int
]
=
None
,
showPlot
:
Boolean
=
false
)
=
{
val
settings
=
summary
.
getSettingsForLibraries
(
runId
,
"flexiprep"
,
keyValues
=
Map
(
"skip_trim"
->
List
(
"skip_trim"
),
"skip_clip"
->
List
(
"skip_clip"
),
"paired"
->
List
(
"paired"
)))
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_trim"
,
None
)
==
Some
(
true
))
...
...
@@ -314,11 +316,23 @@ object FlexiprepReadSummaryReportPage {
val
clipCount
=
settings
.
count
(
_
.
_2
.
getOrElse
(
"skip_clip"
,
None
)
==
Some
(
false
))
val
librariesCount
=
libraries
.
size
/* Todo: Map this conditionally */
if
(
showPlot
){
val
flexiprepReportPlotRead1
:
Option
[
Unit
]
=
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R1"
,
"R1"
,
summary
,
sampleId
=
sampleId
))
if
(
paired
)
{
val
flexiprepReportPlotRead2
:
Option
[
Unit
]
=
Some
(
FlexiprepReport
.
readSummaryPlot
(
outputDir
,
"QC_Reads_R2"
,
"R2"
,
summary
,
sampleId
=
sampleId
))
else
val
flexiprepReportPlotRead2
:
Option
[
Unit
]
=
None
else
val
flexiprepReportPlotRead1
:
Option
[
Unit
]
=
None
}
}
Map
(
"summary"
->
summary
,
"outputDir"
->
outputDir
,
"runId"
->
runId
,
"sampleId"
->
sampleId
,
"libId"
->
libId
,
"showPlot"
"settings"
->
settings
,
"samples"
->
samples
,
"libraries"
->
libraries
,
...
...
@@ -327,13 +341,7 @@ object FlexiprepReadSummaryReportPage {
"librariesCount"
->
librariesCount
)
}
def
settings
(
summary
:
SummaryDb
,
runId
:
Int
)
=
{
}
def
paired
(
summary
:
SummaryDb
,
runId
:
Int
,
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
])
=
}
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