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biopet.biopet
Commits
ea9fe977
Commit
ea9fe977
authored
Feb 19, 2015
by
Peter van 't Hof
Browse files
Changed executables for summary
parent
a61296b2
Changes
4
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
ea9fe977
...
...
@@ -61,17 +61,6 @@ trait SummaryQScript extends BiopetQScript {
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
addChecksum
(
file
)
for
((
_
,
sl
)
<-
summarizables
)
{
for
(
s
<-
sl
)
{
s
match
{
case
c
:
BiopetCommandLineFunctionTrait
=>
{
executables
+=
c
.
configName
->
(
new
File
(
c
.
executable
),
c
.
getVersion
)
}
case
_
=>
}
}
}
for
((
_
,
file
)
<-
this
.
summaryFiles
)
addChecksum
(
file
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
ea9fe977
...
...
@@ -48,10 +48,17 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val
pipelineMap
=
{
val
files
=
parseFiles
(
qscript
.
summaryFiles
)
val
settings
=
qscript
.
summarySettings
val
executables
=
{
for
((
name
,
(
file
,
version
))
<-
qscript
.
executables
)
yield
{
name
->
Map
(
"version"
->
version
,
"md5"
->
BiopetCommandLineFunctionTrait
.
executableMd5Cache
.
getOrElse
(
file
.
getCanonicalPath
,
"N/A"
))
}
val
executables
:
Map
[
String
,
Any
]
=
{
(
for
(
f
<-
qscript
.
functions
if
f
.
isInstanceOf
[
BiopetCommandLineFunctionTrait
])
yield
{
f
match
{
case
f
:
BiopetCommandLineFunctionTrait
=>
{
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
,
"md5"
->
BiopetCommandLineFunctionTrait
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
))
}
case
_
=>
throw
new
IllegalStateException
(
"This should not be possible"
)
}
}).
toMap
}
val
map
=
Map
(
qscript
.
summaryName
->
((
if
(
settings
.
isEmpty
)
Map
[
String
,
Any
]()
else
Map
(
"settings"
->
settings
))
++
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
ea9fe977
...
...
@@ -19,6 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BwaMem
(
val
root
:
Configurable
)
extends
Bwa
{
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
ea9fe977
...
...
@@ -94,7 +94,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".summary.json"
)
def
summaryFiles
=
Map
()
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_bamfile"
->
finalBamFile
,
"input_R1"
->
input_R1
)
++
(
if
(
input_R2
.
isDefined
)
Map
(
"input_R2"
->
input_R2
.
get
)
else
Map
())
def
summarySettings
=
Map
(
"skip_metrics"
->
skipMetrics
,
...
...
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