flexiprepReadSummary.ssp 4.46 KB
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#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
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#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
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<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
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<%@ var rootPath: String %>
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<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
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#{
    val samples = sampleId match {
        case Some(sample) => List(sample.toString)
        case _ => summary.samples.toList
    }
}#
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#if (showPlot)
    #{
        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
    }#
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    <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">
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        #if (showTable)
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            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Hide table</button>
        #else
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            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Show table</button>
        #end
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        <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>
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#end
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<div class="panel-body collapse #if (showTable)in#end" id="QC_ReadsTable">
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<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
    <thead><tr>
        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
        <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>
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</table>
</div>