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biopet.biopet
Commits
2483b207
Commit
2483b207
authored
Oct 28, 2015
by
Peter van 't Hof
Browse files
Fixed report
parent
a6ff2665
Changes
2
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public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
View file @
2483b207
...
...
@@ -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>${summary.getValue("shivavariantcalling", "settings", "variantcallers").get
OrElse(List("None"))
.asInstanceOf[List[String]].mkString(", ")}</td>
</tr>
<tr><th>Reference</th><td>${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>
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
2483b207
...
...
@@ -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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