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biopet.biopet
Commits
e07267db
Commit
e07267db
authored
Aug 15, 2015
by
Peter van 't Hof
Browse files
Skipping parts of report when they are skipped in the pipeline
parent
0ae99234
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
e07267db
...
...
@@ -35,18 +35,22 @@ object MappingReport extends ReportBuilder {
/** Root page for single BamMetrcis report */
def
indexPage
=
{
val
bamMetricsPage
=
BammetricsReport
.
bamMetricsPage
(
summary
,
sampleId
,
libId
)
ReportPage
(
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
:::
bamMetricsPage
.
subPages
:::
List
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
()),
"Files"
->
ReportPage
(
List
(),
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"
),
"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
))
),
Map
())
),
List
(
val
skipFlexiprep
=
summary
.
getValue
(
sampleId
,
libId
,
"mapping"
,
"settings"
,
"skip_flexiprep"
).
getOrElse
(
false
)
==
true
val
bamMetricsPage
=
if
(
summary
.
getValue
(
sampleId
,
libId
,
"mapping"
,
"settings"
,
"skip_metrics"
).
getOrElse
(
false
)
==
true
)
{
Some
(
BammetricsReport
.
bamMetricsPage
(
summary
,
sampleId
,
libId
))
}
else
None
ReportPage
((
if
(
skipFlexiprep
)
Nil
else
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
))
:::
bamMetricsPage
.
map
(
_
.
subPages
).
getOrElse
(
Nil
)
:::
List
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
()),
"Files"
->
ReportPage
(
List
(),
(
if
(
skipFlexiprep
)
Nil
else
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"
),
"After QC fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"
)))
:::
List
(
"Bam files per lib"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"
,
Map
(
"sampleLevel"
->
false
))
),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp"
)
)
:::
bamMetricsPage
.
sections
,
)
:::
bamMetricsPage
.
map
(
_
.
sections
).
getOrElse
(
Nil
)
,
Map
()
)
}
...
...
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