Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
b4b21a18
Commit
b4b21a18
authored
Sep 20, 2016
by
Peter van 't Hof
Browse files
Fix summary
parent
d71e3968
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
b4b21a18
...
...
@@ -45,10 +45,12 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
krakenReportJSON
.
skipNames
=
config
(
"skipNames"
,
default
=
false
)
add
(
krakenReportJSON
)
addSummarizable
(
krakenReportJSON
,
"centrifugereport"
)
addSummaryJobs
()
}
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".
kraken
.summary.json"
)
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".
centrifuge
.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
()
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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