flexiprepBaseSummary.ssp 7.59 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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<%@ var showIntro: Boolean = true %>
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#{
    val samples = sampleId match {
        case Some(sample) => List(sample.toString)
        case _ => summary.samples.toList
    }
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}#
#{
    def flexiprepConfig: String = {
    val skip_trim = summary.getLibraryValues("flexiprep", "settings", "skip_trim")
    val skip_clip = summary.getLibraryValues("flexiprep", "settings", "skip_clip")

    // this means both adaptor trimming and clipping are enabled
    if(skip_clip.forall(_._2 == Some(false)) && skip_trim.forall(_._2 == Some(false))) "trim_clip"
    // This means everything was disabled
    else if(skip_clip.forall(_._2 == Some(true)) && skip_trim.forall(_._2 == Some(true))) "None"
    // this means trimming was partially disabled, but not clipping
    else if(skip_trim.exists(_._2 == Some(true)) && skip_clip.map(_._2).toList.distinct.size == 1) "partial_trim"
    //this means clipping was partially disabled, but not trimming
    else if(skip_clip.exists(_._2 == Some(true)) && skip_trim.map(_._2).toList.distinct.size == 1) "partial_clip"
    // this means both trimming and clipping were partially disabled
    else "partial_both"
    }

    /**
    * TODO: This should probably be an enum in stead.
    * It's likely best to do this in a separate reporting module rather than in one big jar.
    */
    val flexiprepConfigMap = Map(
    "trim_clip" -> """You have selected both <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> as pre-processing steps""",
    "None" -> """You have selected no pre-processing step to be performed""",
    "partial_trim" ->  """You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming </a> off for some libraries, but not all.""",
    "partial_clip" -> """You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> for some libraries, but not all.""",
    "partial_both" ->  """You have chosen to turn <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Alternative_clipping_strategies_.28Adaptor_clipping.29">adaptor clipping</a> and <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Pre-processing#Sequence_Quality_Trimming">read trimming</a> off for some libraries, but not all."""
    )

    val flexiprepDisplayed = flexiprepConfigMap(flexiprepConfig)


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}#
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#if (showIntro)
    <br/>
    <div class="row">
    <div class="col-md-1"></div>
    <div class="col-md-6">
        <p>
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        ${unescape(flexiprepDisplayed)}
        </p>
        <p>
        #if(sampleId.isDefined && libId.isDefined)
            Here we show aggregated quality statistics sequencing library ${libId} for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
        #elseif(sampleId.isDefined)
            Here we show aggregated quality statistics for every sequencing library for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
        #else
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            Here we show aggregated quality statistics for every sequencing library. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads.
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        #end
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        </p>
    </div>
    </div>
#end
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#if (showPlot)
    #{
        FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R1","R1", summary, sampleId = sampleId)
        FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_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_Bases_R1.png" class="img-responsive" />
            </div>
            <div class="col-sm-6 col-md-6">
                <img src="QC_Bases_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_BasesTable">Hide table</button>
        #else
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            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_BasesTable">Show table</button>
        #end
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        <i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_R1.tsv">R1 reads stats</a> -
        <i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_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_BasesTable">
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<!-- Table -->
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<table class="table sortable-theme-bootstrap">
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    <thead><tr>
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        <th>Sample</th>
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        <th colspan="2">Library</th>
        <th>Before QC</th>
        <th>Discarded</th>
        <th>(%)</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, "bases", "num_total").getOrElse(0).asInstanceOf[Long]
                            val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
                        }#
                        <td>${read}</td>
                        <td>${beforeTotal}</td>
                        <td>${beforeTotal - afterTotal}</td>
                        <td>${(beforeTotal - afterTotal).toDouble / beforeTotal * 100}%</td>
                        <td>${afterTotal}</td>
                    #end
                </tr>
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            #end
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        #end
    </tbody>
</table>
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</div>