multisampleMappingFront.ssp 1.97 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
Peter van 't Hof's avatar
Peter van 't Hof committed
2
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
Peter van 't Hof's avatar
Peter van 't Hof committed
3
4
5
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
Peter van 't Hof's avatar
Peter van 't Hof committed
6
<%@ var rootPath: String %>
7
<%@ var pipeline: String %>
Peter van 't Hof's avatar
Peter van 't Hof committed
8
9
10
11
12
13
14
15
16
17
18
<%@ var runId: Int %>
#{
    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
    val settings = summary.getSettingKeys(runId, Right(pipeline),
    keyValues = Map(
        "contigs" -> List("reference", "contigs"),
        "species" -> List("reference", "species"),
        "name" -> List("reference", "name")
    ))
}#
Peter van 't Hof's avatar
Peter van 't Hof committed
19
20
<table class="table">
<tbody>
Wai Yi Leung's avatar
Wai Yi Leung committed
21
    <tr><th>Pipeline</th><td>${pipeline}</td></tr>
Peter van 't Hof's avatar
Peter van 't Hof committed
22
23
24
25
26
    <tr><th>Version</th><td>${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>
    <tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
    <tr><th>Number of samples</th><td>${samples.size}</td></tr>
Peter van 't Hof's avatar
Peter van 't Hof committed
27
28
29
30
31
32
33
</tbody>
</table>
<br/>
<div class="row">
    <div class="col-md-1"></div>
    <div class="col-md-6">
    <p>
34
    In this web document you can find your <em>${pipeline}</em> pipeline report.
Peter van 't Hof's avatar
Peter van 't Hof committed
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
    Different categories of data can be found in the left-side menu.
    Statistics per sample and library can be accessed through the top-level menu.
    Some statistics for target regions can be found in the regions tab.
    Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
    </p>

    <p>
        <small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
            title="Sequence Analysis Support Core">SASC</abbr></a> and <a
        href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
        LUMC.
        </small>
    </p>
    </div>
</div>