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biopet.biopet
Commits
ad33c271
Commit
ad33c271
authored
Sep 20, 2016
by
Peter van 't Hof
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Added centrifuge to report
parent
39647fd4
Changes
3
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3 changed files
with
9 additions
and
4 deletions
+9
-4
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
...urces/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
+3
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
...nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
+1
-1
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+5
-1
No files found.
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
View file @
ad33c271
...
...
@@ -10,11 +10,12 @@
<%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
<%@ var summaryTag: String = "krakenreport" %>
<%
val summaries = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues("gearskraken", "stats",
"krakenreport"
).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, "gearskraken", "stats",
"krakenreport"
).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
summary.getSampleValues("gearskraken", "stats",
summaryTag
).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, "gearskraken", "stats",
summaryTag
).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
ad33c271
...
...
@@ -44,7 +44,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
krakenReportJSON
.
output
=
new
File
(
outputDir
,
s
"$outputName.krkn.json"
)
krakenReportJSON
.
skipNames
=
config
(
"skipNames"
,
default
=
false
)
add
(
krakenReportJSON
)
addSummarizable
(
krakenReportJSON
,
"centrifugereport"
)
addSummarizable
(
krakenReportJSON
,
"centrifuge
_
report"
)
addSummaryJobs
()
}
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
ad33c271
...
...
@@ -38,13 +38,17 @@ object GearsReport extends MultisampleReportBuilder {
def
indexPage
=
{
val
krakenExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"krakenreport"
).
values
.
forall
(
_
.
isDefined
)
val
centrifugeExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"centrifuge_report"
).
values
.
forall
(
_
.
isDefined
)
val
qiimeClosesOtuTable
=
summary
.
getValue
(
"gears"
,
"files"
,
"pipeline"
,
"qiime_closed_otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
"gears"
,
"files"
,
"pipeline"
,
"qiime_open_otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
(
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
(
"summaryTag"
->
"centriguge_report"
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
...
...
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