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biopet.biopet
Commits
59100477
Commit
59100477
authored
Mar 29, 2017
by
Peter van 't Hof
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Removing unused templates
parent
68751188
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51 deletions
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bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
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-22
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
.../sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
+0
-20
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp
...urces/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp
+0
-3
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
...esources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
+0
-3
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
...urces/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
+0
-3
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
deleted
100644 → 0
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68751188
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var fields: List[String] = List("All", "Mapped", "Duplicates", "MAPQ>30", "MateUnmapped", "Mate on other chr")%>
<table>
<tbody>
#for (field <- fields)
<tr><th>${field}</th><td>
#if (libId.isDefined)
${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
#else
${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
#end
</td></tr>
#end
</tbody>
</table>
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
deleted
100644 → 0
View file @
68751188
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] = None %>
<%@ var metricsTag: String = "bammetrics" %>
<table class="table sortable-theme-bootstrap">
<thead><tr>
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
<tr>
<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "path")}</td>
<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "md5")}</td>
</tr>
</tbody>
</table>
\ No newline at end of file
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp
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68751188
#{ //TODO: Need content }#
Todo
\ No newline at end of file
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
deleted
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68751188
#{ //TODO: Need content }#
Todo
\ No newline at end of file
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
deleted
100644 → 0
View file @
68751188
#{ //TODO: Need content }#
Todo
\ No newline at end of file
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