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biopet.biopet
Commits
4e394bc9
Commit
4e394bc9
authored
Jul 25, 2017
by
Ruben Vorderman
Browse files
Start on defuturing readsummaryplot
parent
83188c3f
Changes
2
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
4e394bc9
...
...
@@ -67,6 +67,10 @@
#end
#if (showPlot)
#{
FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
if (paired) FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
}#
<div class="panel-body">
<div class="row">
<div class="col-sm-6 col-md-6">
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
4e394bc9
...
...
@@ -16,13 +16,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepReadSummary
,
FlexiprepReport
}
import
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
...
...
@@ -145,6 +140,8 @@ object GearsReport extends MultisampleReportBuilder {
"biomFile"
->
new
File
(
run
.
outputDir
+
File
.
separator
+
qiimeOpenOtuTable
.
get
.
path
))
)))
else
None
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
true
,
false
)
Future
{
ReportPage
(
List
(
centrifugePage
,
krakenPage
,
qiimeClosedPage
,
qiimeOpenPage
).
flatten
:::
List
(
...
...
@@ -154,7 +151,7 @@ object GearsReport extends MultisampleReportBuilder {
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)
),
flexiprepReadSummary
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
))
...
...
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