Commit 2483b207 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed report

parent a6ff2665
......@@ -11,7 +11,7 @@
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
<tr>
<th>Variantcallers</th>
<td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]].mkString(", ")}</td>
<td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").getOrElse(List("None")).asInstanceOf[List[String]].mkString(", ")}</td>
</tr>
<tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
......
......@@ -120,9 +120,10 @@ object ShivaReport extends MultisampleReportBuilder {
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam")),
"VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
), Map())
Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))) ++
(if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
Map("sampleId" -> None))) else Nil)
, Map())
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
......
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