flexiprepReadSummary.ssp 4.84 KB
Newer Older
1 2
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
3 4
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
5 6 7
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
8
<%@ var rootPath: String %>
9 10 11
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
Peter van 't Hof's avatar
Peter van 't Hof committed
12
<%@ var showIntro: Boolean = true %>
13 14 15 16 17 18
#{
    val samples = sampleId match {
        case Some(sample) => List(sample.toString)
        case _ => summary.samples.toList
    }
}#
Peter van 't Hof's avatar
Peter van 't Hof committed
19 20 21 22 23 24
#if (showIntro)
    <br/>
    <div class="row">
    <div class="col-md-1"></div>
    <div class="col-md-6">
        <p>
Sander Bollen's avatar
Sander Bollen committed
25
            Here we show aggregated quality statistics for every sequencing library. It shows the total number of reads used after quality control, and the total number of reads discarded during quality control. This is done for both forward and reverse reads.
Peter van 't Hof's avatar
Peter van 't Hof committed
26 27 28 29
        </p>
    </div>
    </div>
#end
30 31 32 33 34 35

#if (showPlot)
    #{
        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
    }#
36 37 38 39 40 41 42 43 44 45 46 47
    <div class="panel-body">
        <div class="row">
            <div class="col-sm-6 col-md-6">
                <img src="QC_Reads_R1.png" class="img-responsive">
            </div>
            <div class="col-sm-6 col-md-6">
                <img src="QC_Reads_R2.png" class="img-responsive">
            </div>
        </div>

    </div>
    <div class="panel-footer">
Peter van 't Hof's avatar
Peter van 't Hof committed
48
        #if (showTable)
Peter van 't Hof's avatar
Peter van 't Hof committed
49 50
            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Hide table</button>
        #else
Peter van 't Hof's avatar
Peter van 't Hof committed
51 52
            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Show table</button>
        #end
53 54 55
        <i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R1.tsv">R1 reads stats</a> -
        <i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R2.tsv">R2 reads stats</a>
    </div>
56
#end
57

Peter van 't Hof's avatar
Peter van 't Hof committed
58
<div class="panel-body collapse #if (showTable)in#end" id="QC_ReadsTable">
59

Peter van 't Hof's avatar
Peter van 't Hof committed
60
<!-- Table -->
Peter van 't Hof's avatar
Peter van 't Hof committed
61
<table class="table sortable-theme-bootstrap">
Peter van 't Hof's avatar
Peter van 't Hof committed
62
    <thead><tr>
Peter van 't Hof's avatar
Peter van 't Hof committed
63
        <th>Sample</th>
Peter van 't Hof's avatar
Peter van 't Hof committed
64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106
        <th colspan="2">Library</th>
        <th>Before QC</th>
        <th>Clipping</th>
        <th>Trimming</th>
        <th>After QC</th>
    </tr></thead>
    <tbody>
        #for (sample <- samples.toList.sorted)
            #{
                val libs = libId match {
                case Some(libId) => List(libId.toString)
                case _ => summary.libraries(sample).toList
                }
                val sampleRowspan = {
                libs.size +
                libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
                }
            }#
            <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
            #for (libId <- libs)
                #if (libs.head != libId) <tr> #end
                    #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
                    <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
                    #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
                    #for (read <- reads)
                        #if (read == "R2") </tr><tr> #end
                        #{
                            val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
                            val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
                            val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).asInstanceOf[Long]
                            val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).asInstanceOf[Long]
                            val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).asInstanceOf[Long]
                        }#
                        <td>${read}</td>
                        <td>${beforeTotal}</td>
                        <td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
                        <td>${trimmingDiscarded}</td>
                        <td>${afterTotal}</td>
                    #end
                </tr>
            #end
        #end
    </tbody>
107

Peter van 't Hof's avatar
Peter van 't Hof committed
108 109
</table>
</div>