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
d222ae11
Commit
d222ae11
authored
Oct 29, 2015
by
Peter van 't Hof
Browse files
Added a merge step
parent
5c207b0b
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
d222ae11
...
...
@@ -20,7 +20,7 @@ import java.io.{ File, PrintWriter }
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.
{
LastCommitHash
,
Version
}
import
nl.lumc.sasc.biopet.LastCommitHash
import
org.broadinstitute.gatk.queue.function.
{
InProcessFunction
,
QFunction
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -90,7 +90,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
}
(
qscript
.
functions
.
flatMap
(
fetchVersion
(
_
)
)
++
qscript
.
functions
.
flatMap
(
fetchVersion
)
++
qscript
.
functions
.
flatMap
{
case
f
:
BiopetCommandLineFunction
=>
f
.
pipesJobs
...
...
@@ -99,28 +99,28 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
).
toMap
}
val
map
=
Map
(
qscript
.
summaryName
->
(
Map
(
val
map
=
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
settings
,
"files"
->
Map
(
"pipeline"
->
files
),
"executables"
->
executables
.
toMap
)
)
"executables"
->
executables
.
toMap
)
)
qscript
match
{
case
tag
:
SampleLibraryTag
=>
prefixSampleLibrary
(
map
,
tag
.
sampleId
,
tag
.
libId
)
case
q
:
MultiSampleQScript
=>
{
Map
(
"samples"
->
q
.
samples
.
map
{
case
(
sampleName
,
sample
)
=>
sampleName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
sample
.
summarySettings
),
"libraries"
->
sample
.
libraries
.
map
{
case
(
libName
,
lib
)
=>
sampleName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
lib
)
)
}
)
})
++
map
}
case
q
:
MultiSampleQScript
=>
ConfigUtils
.
mergeMaps
(
Map
(
"samples"
->
q
.
samples
.
map
{
case
(
sampleName
,
sample
)
=>
sampleName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
sample
.
summarySettings
),
"libraries"
->
sample
.
libraries
.
map
{
case
(
libName
,
lib
)
=>
sampleName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
lib
.
summarySettings
)
)
}
)
}),
map
)
case
_
=>
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