Commit 51b147c0 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix: Show a message for those plot, which were not created by FastQC. Some...

Fix: Show a message for those plot, which were not created by FastQC. Some statistics cannot be collected by FastQC such as Kmer when the sequences are clean.
parent ede07209
......@@ -14,14 +14,22 @@
def getPlot(read:String) = {
summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "path").collect {
case value => {
val file = new File(value.toString)
case path => {
val file = new File(path.toString)
val newFile = new File(outputDir, read + "_" + file.getName)
if (file.exists()) FileUtils.copyFile(file, newFile)
newFile.getName
}
}
}
def plotAvailable(read:String) = {
summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "md5").collect {
case md5 if md5 != "error_on_capture" => true
case otherwise => false
}.getOrElse(false)
}
}#
<div class="row">
......@@ -32,11 +40,19 @@
<div class="row">
<div class="col-md-1"><b>R1</b></div>
<div class="col-md-5">
#if (plotAvailable( "fastqc_R1" ))
<img class="img-responsive" src="${getPlot("fastqc_R1")}" />
#else
Image was not generated by FastQC
#end
</div>
#if (!skipTrim || !skipClip)
<div class="col-md-5">
#if (plotAvailable( "fastqc_R1_qc" ))
<img class="img-responsive" src="${getPlot("fastqc_R1_qc")}" />
#else
Image was not generated by FastQC
#end
</div>
#end
</div>
......@@ -44,11 +60,19 @@
<div class="row">
<div class="col-md-1"><b>R2</b></div>
<div class="col-md-5">
#if (plotAvailable( "fastqc_R2" ))
<img class="img-responsive" src="${getPlot("fastqc_R2")}" />
#else
Image was not generated by FastQC
#end
</div>
#if (!skipTrim || !skipClip)
<div class="col-md-5">
#if (plotAvailable( "fastqc_R2_qc" ))
<img class="img-responsive" src="${getPlot("fastqc_R2_qc")}" />
#else
Image was not generated by FastQC
#end
</div>
#end
</div>
......
......@@ -62,7 +62,7 @@ object FlexiprepReport extends ReportBuilder {
fastqcPlotSection("Sequence quality", "plot_per_sequence_quality"),
fastqcPlotSection("Base GC content", "plot_per_base_gc_content"),
fastqcPlotSection("Sequence GC content", "plot_per_sequence_gc_content"),
fastqcPlotSection("Base seqeunce content", "plot_per_base_sequence_content"),
fastqcPlotSection("Base sequence content", "plot_per_base_sequence_content"),
fastqcPlotSection("Duplication", "plot_duplication_levels"),
fastqcPlotSection("Kmers", "plot_kmer_profiles"),
fastqcPlotSection("Length distribution", "plot_sequence_length_distribution")
......@@ -71,7 +71,7 @@ object FlexiprepReport extends ReportBuilder {
)
protected def fastqcPlotSection(name: String, tag: String) = {
name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp", Map("plot" -> tag))
name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp", Map("plot" -> tag))
}
/**
......
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