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biopet.biopet
Commits
776769bf
Commit
776769bf
authored
Apr 09, 2015
by
Peter van 't Hof
Browse files
Extended flexiprep summaries
parent
a8ebd299
Changes
7
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/biopet.css
View file @
776769bf
...
...
@@ -92,6 +92,7 @@ footer {
table
,
td
,
th
{
border
:
1px
solid
green
;
border-collapse
:
collapse
;
padding
:
2px
;
}
th
{
background-color
:
green
;
...
...
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @
776769bf
...
...
@@ -39,7 +39,7 @@
</head>
<body>
<header><h1>
${reportName}
</h1></header>
<!--
<header><h1>${reportName}</h1></header>
-->
<nav
id=
"menu"
>
<ul>
#for (t
<-
0
to
path.size
)
...
...
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp
→
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprep
Base
Summary.ssp
View file @
776769bf
...
...
@@ -12,12 +12,10 @@
<table>
<thead><tr>
<th>Sample</th>
<th>Library</th>
<th>Read</th>
<th>Reads before QC</th>
<th>Bases before QC</th>
<th>Reads after QC</th>
<th>Bases after QC</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th colspan="2">Discarded</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
...
...
@@ -37,19 +35,19 @@
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end>${libId}</td>
<td>R1</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1", "reads", "num_total")} </td>
<td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1", "bases", "num_total")}
</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1_after", "reads", "num_total")}</td>
<td> ${
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_
R1_after"
, "bases", "num_total")
}</td>
#if (pai
red
== true)
</tr><tr>
<td>R2
</td>
<td>${
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2", "reads", "num_t
otal
")
}</td>
<td>
${
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2", "bases", "num_t
otal
")
}</td>
<td>${
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2_after", "reads", "num_total")}
</td>
<td>
${
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2_after", "bases", "num_t
otal
")
}</td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal =
summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_
" + read
, "bases", "num_total")
.getOrElse(0).asInstanceOf[Long]
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" +
re
a
d
+ "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
}#
<td>${read}
</td>
<td>${
beforeT
otal}</td>
<td>${
beforeTotal - afterT
otal}</td>
<td>${
(beforeTotal - afterTotal).toDouble / beforeTotal * 100}%
</td>
<td>${
afterT
otal}</td>
#end
</tr>
#end
...
...
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
View file @
776769bf
...
...
@@ -28,7 +28,7 @@
<tbody>
<tr><td></td>
<th>Before QC</th>
#if (!skipTrim || !skipClip) <th>
a
fter QC</th> #end
#if (!skipTrim || !skipClip) <th>
A
fter QC</th> #end
</tr>
<tr><th>R1</th>
<td><img src="${getPlot("fastqc_R1")}" width="75%"></td>
...
...
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
0 → 100644
View file @
776769bf
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
}#
<table>
<thead><tr>
<th>Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}">${sample}</td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end>${libId}</td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
<td>${read}</td>
<td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")}
</td>
<td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")}</td>
#end
</tr>
#end
#end
</tbody>
</table>
\ No newline at end of file
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
776769bf
...
...
@@ -10,7 +10,8 @@ object FlexiprepReport extends ReportBuilder {
def
indexPage
=
{
ReportPage
(
Map
(),
List
(
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp"
),
"Read Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"Base Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
),
fastqcPlotSection
(
"Base quality"
,
"plot_per_base_quality"
),
fastqcPlotSection
(
"Sequence quality"
,
"plot_per_sequence_quality"
),
fastqcPlotSection
(
"Base GC content"
,
"plot_per_base_gc_content"
),
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
776769bf
...
...
@@ -9,19 +9,25 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
object
ShivaReport
extends
MultisampleReportBuilder
{
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
=
{
ReportPage
(
Map
(
"Libraries"
->
generateLibraryPage
(
args
)),
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
)
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
),
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
def
libraryPage
(
libId
:
String
,
args
:
Map
[
String
,
Any
])
=
{
ReportPage
(
Map
(
"Flexiprep"
->
FlexiprepReport
.
indexPage
),
List
(),
args
)
ReportPage
(
Map
(
"Flexiprep"
->
FlexiprepReport
.
indexPage
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
def
reportName
=
"Title Test"
def
generalPage
=
ReportPage
(
Map
(),
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
),
"Flexiprep"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp"
)
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
Map
())
// FIXME: Not yet finished
...
...
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