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
4350c5b5
Commit
4350c5b5
authored
Oct 06, 2015
by
Wai Yi Leung
Browse files
Adding files to summary json
parent
b674053a
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
View file @
4350c5b5
...
...
@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
,
Input
}
/**
* KrakenReportToJson function class for usage in Biopet pipelines
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
4350c5b5
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import
nl.lumc.sasc.biopet.extensions.tools.
{
KrakenReportToJson
,
FastqSync
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
KrakenReportToJson
,
FastqSync
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -120,11 +120,6 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
krakenReportJSON
.
skipNames
=
config
(
"skipNames"
,
default
=
true
)
add
(
krakenReportJSON
)
// val krakenReportJSON = new KrakenReportToJson(qscript)
// krakenReportJSON.input = krakenReport.output
// krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
// add(krakenReportJSON)
addSummaryJobs
()
}
...
...
@@ -135,7 +130,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
def
summarySettings
=
Map
()
/** Files for the summary */
def
summaryFiles
=
(
if
(
bamFile
.
isDefined
)
Map
(
"input_bam"
->
bamFile
.
get
)
else
Map
())
++
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
.
empty
++
(
if
(
bamFile
.
isDefined
)
Map
(
"input_bam"
->
bamFile
.
get
)
else
Map
())
++
(
if
(
fastqFileR1
.
isDefined
)
Map
(
"input_R1"
->
fastqFileR1
.
get
)
else
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