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biopet.biopet
Commits
32e20bf4
Commit
32e20bf4
authored
Mar 10, 2017
by
Peter van 't Hof
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Fixing gears templates
parent
106b05f0
Changes
4
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4 changed files
with
38 additions
and
24 deletions
+38
-24
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
...ources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
+13
-7
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
.../nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
+14
-8
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+10
-8
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
...es/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
+1
-1
No files found.
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
View file @
32e20bf4
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Gears</td></tr>
<tr><th>Version</th><td>${
summary.getValue("meta", "pipeline_version")
}</td></tr>
<tr><th>Last commit hash</th><td>${
summary.getValue("meta", "last_commit_hash")
}</td></tr>
<tr><th>Output directory</th><td>${
summary.getValue("meta", "output_dir")
}</td></tr>
<tr><th>Version</th><td>${
run.version
}</td></tr>
<tr><th>Last commit hash</th><td>${
run.commitHash
}</td></tr>
<tr><th>Output directory</th><td>${
run.outputDir
}</td></tr>
</tbody>
</table>
<br/>
...
...
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
View file @
32e20bf4
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var runId: Int %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Gears</td></tr>
<tr><th>Version</th><td>${
summary.getValue("meta", "pipeline_version")
}</td></tr>
<tr><th>Last commit hash</th><td>${
summary.getValue("meta", "last_commit_hash")
}</td></tr>
<tr><th>Output directory</th><td>${
summary.getValue("meta", "output_dir")
}</td></tr>
<tr><th>Pipeline</th><td>Gears
Single
</td></tr>
<tr><th>Version</th><td>${
run.version
}</td></tr>
<tr><th>Last commit hash</th><td>${
run.commitHash
}</td></tr>
<tr><th>Output directory</th><td>${
run.outputDir
}</td></tr>
#if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
#if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
</tbody>
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
32e20bf4
...
...
@@ -14,11 +14,13 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
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.utils.config.Configurable
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.
{
NoLibrary
,
NoModule
,
SampleId
}
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
...
...
@@ -57,10 +59,10 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeClosesOtuTable
.
get
.
path
)
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeOpenOtuTable
.
get
.
path
)
)))
else
Nil
)
:::
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Versions"
->
ReportPage
(
List
(),
List
(
...
...
@@ -97,10 +99,10 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeClosesOtuTable
.
get
.
path
)
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeOpenOtuTable
.
get
.
path
)
)))
else
Nil
)
:::
List
(
"Libraries"
->
generateLibraryPage
(
args
)
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
...
...
@@ -133,10 +135,10 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeClosesOtuTable
.
get
.
path
)
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
)),
Map
(
"biomFile"
->
new
File
(
qiimeOpenOtuTable
.
get
.
path
)
)))
else
Nil
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
...
...
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
View file @
32e20bf4
...
...
@@ -20,7 +20,7 @@
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>
${run.name}
</td></tr>
<tr><th>Pipeline</th><td>
Mapping
</td></tr>
<tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${run.outputDir}</td></tr>
...
...
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