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biopet.biopet
Commits
3d39733e
Commit
3d39733e
authored
Dec 25, 2015
by
Peter van 't Hof
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Added krona plot for cqiime closed to gears report
parent
c8012021
Changes
1
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1 changed file
with
21 additions
and
4 deletions
+21
-4
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+21
-4
No files found.
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
3d39733e
package
nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
nl.lumc.sasc.biopet.core.report.
{
ReportSection
,
ReportPage
,
MultisampleReportBuilder
,
ReportBuilderExtension
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -21,11 +23,16 @@ object GearsReport extends MultisampleReportBuilder {
def
indexPage
=
{
val
krakenExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"krakenreport"
).
values
.
forall
(
_
.
isDefined
)
val
qiimeClosesOtuTable
=
summary
.
getValue
(
"gears"
,
"files"
,
"pipeline"
,
"qiime_closed_otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
(
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kr
aken analysis
"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
(
if
(
krakenExecuted
)
List
(
"Kraken
analysis
"
->
ReportPage
(
List
(),
List
(
"Kr
ona plot
"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
)
:::
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Versions"
->
ReportPage
(
List
(),
List
(
...
...
@@ -47,10 +54,15 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
((
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
)
:::
List
(
"Libraries"
->
generateLibraryPage
(
args
)
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
...
...
@@ -61,12 +73,17 @@ object GearsReport extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
,
List
(
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
...
...
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