Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
618ebeda
Commit
618ebeda
authored
Jul 26, 2017
by
Ruben Vorderman
Browse files
Fix flexiprep bug and remove import ugliness in gears report
parent
f1dc8c0f
Changes
3
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
618ebeda
...
...
@@ -14,7 +14,6 @@
<%@ var multisample: Boolean = true %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
<%-- variables to be added to remove dependency upon futures --%>
<%@ var settings: Map[(Int, Int), Map[String, Option[Any]]] %>
<%@ var paired: Boolean %>
<%@ var samples: Seq[Sample] %>
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
618ebeda
...
...
@@ -295,8 +295,8 @@ object FlexiprepReadSummary {
FlexiprepReport
.
readSummaryPlotLines
(
"R2"
,
summary
,
sampleId
=
sampleId
)
val
seqstatPaths
=
Map
(
"num_total"
->
List
(
"reads"
,
"num_total"
))
val
clippingPaths
=
Map
(
"num_reads_discarded_too_
short
"
->
List
(
"num_reads_discarded_too_
short
"
))
val
clippingPaths
=
Map
(
"num_reads_discarded_too_short"
->
List
(
"num_reads_discarded_too_short"
),
"num_reads_discarded_too_
long
"
->
List
(
"num_reads_discarded_too_
long
"
))
val
trimmingPaths
=
Map
(
"num_reads_discarded"
->
List
(
"num_reads_discarded_total"
))
val
seqstatStats
:
Map
[(
Int
,
Int
)
,
Map
[
String
,
Option
[
Any
]]]
=
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
618ebeda
...
...
@@ -16,36 +16,17 @@ 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.pipelines.gears
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepBaseSummary
,
FlexiprepReadSummary
,
FlexiprepReport
}
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepBaseSummary
,
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.Schema.
{
Library
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
NoLibrary
,
NoModule
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
ModuleName
,
NoLibrary
,
NoModule
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.Library
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample
import
scala.concurrent.
{
Await
,
Future
}
import
scala.concurrent.duration.Duration
import
scala.concurrent.
{
Await
,
Future
}
/**
* Report for Gears
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment