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biopet.biopet
Commits
48b70e4b
Commit
48b70e4b
authored
Jun 16, 2015
by
Peter van 't Hof
Browse files
Added framework for target report
parent
f048ba61
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
48b70e4b
...
...
@@ -21,13 +21,14 @@ object ShivaReport extends MultisampleReportBuilder {
// FIXME: Not yet finished
def
indexPage
=
{
val
regions
=
regionsPage
ReportPage
(
Map
(
"Samples"
->
generateSamplesPage
(
pageArgs
),
"Files"
->
filesPage
,
"Versions"
->
ReportPage
(
Map
(),
List
((
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
))),
Map
())
Map
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
(
if
(
regions
.
isDefined
)
Map
(
regions
.
get
)
else
Map
())
++
Map
(
"Files"
->
filesPage
,
"Versions"
->
ReportPage
(
Map
(),
List
((
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
))),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"
),
...
...
@@ -47,6 +48,32 @@ object ShivaReport extends MultisampleReportBuilder {
)
}
def
regionsPage
=
{
val
roi
=
summary
.
getValue
(
"shiva"
,
"settings"
,
"regions_of_interest"
)
val
amplicon
=
summary
.
getValue
(
"shiva"
,
"settings"
,
"amplicon_bed"
)
var
regionPages
:
Map
[
String
,
ReportPage
]
=
Map
()
def
createPage
(
name
:
String
,
amplicon
:
Boolean
=
false
)
:
ReportPage
=
{
//TODO: get target content
ReportPage
(
Map
(),
List
(),
Map
())
}
amplicon
match
{
case
Some
(
x
:
String
)
=>
regionPages
+=
(
x
+
" (Amplicon)"
)
->
createPage
(
x
,
true
)
case
_
=>
}
roi
match
{
case
Some
(
x
:
String
)
=>
regionPages
+=
x
->
createPage
(
x
,
false
)
case
Some
(
x
:
List
[
_
])
=>
x
.
foreach
(
x
=>
regionPages
+=
x
.
toString
->
createPage
(
x
.
toString
,
false
))
case
_
=>
}
if
(
regionPages
.
nonEmpty
)
Some
(
"Regions"
->
ReportPage
(
regionPages
,
List
(),
Map
()))
else
None
}
def
filesPage
=
ReportPage
(
Map
(),
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"
),
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
48b70e4b
...
...
@@ -293,7 +293,15 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def
summaryFile
=
new
File
(
outputDir
,
"Shiva.summary.json"
)
/** Settings of pipeline for summary */
def
summarySettings
=
Map
()
def
summarySettings
=
{
val
roiBedFiles
:
List
[
File
]
=
config
(
"regions_of_interest"
,
Nil
)
val
ampliconBedFile
:
Option
[
File
]
=
config
(
"amplicon_bed"
)
Map
(
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
))
)
}
/** Files for the summary */
def
summaryFiles
=
Map
()
...
...
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