Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
e7437482
Commit
e7437482
authored
Sep 20, 2016
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Added sample and library plots
parent
139202a4
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
16 additions
and
2 deletions
+16
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+16
-2
No files found.
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
e7437482
...
...
@@ -81,12 +81,19 @@ 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
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearscentrifuge"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearsqiimeopen"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
((
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
ReportPage
((
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(
"Non-unique"
->
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
else
Nil
)
:::
(
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
(
...
...
@@ -106,6 +113,7 @@ object GearsReport extends MultisampleReportBuilder {
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
flexiprepExecuted
=
summary
.
getLibraryValue
(
sampleId
,
libId
,
"flexiprep"
).
isDefined
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearscentrifuge"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearsqiimeopen"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
...
...
@@ -113,7 +121,13 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage
(
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(
"Non-unique"
->
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
else
Nil
)
:::
(
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
(
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment