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
2a67db54
Commit
2a67db54
authored
Oct 13, 2015
by
Peter van 't Hof
Browse files
Added version check for pipe jobs
parent
1f0fcf1a
Changes
3
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
2a67db54
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.core.
{
Version
,
CommandLineResources
,
Reference
,
BiopetJavaCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.
{
Version
,
CommandLineResources
,
Reference
,
BiopetJavaCommandLineFunction
}
import
org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
View file @
2a67db54
...
...
@@ -51,6 +51,9 @@ class BiopetFifoPipe(val root: Configurable,
deps
:::=
inputs
.
values
.
toList
.
flatten
.
filter
(!
fifoFiles
.
contains
(
_
))
deps
=
deps
.
distinct
pipesJobs
:::=
commands
pipesJobs
=
pipesJobs
.
distinct
}
override
def
beforeCmd
()
:
Unit
=
{
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
2a67db54
...
...
@@ -71,23 +71,29 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val
files
=
parseFiles
(
qscript
.
summaryFiles
)
val
settings
=
qscript
.
summarySettings
val
executables
:
Map
[
String
,
Any
]
=
{
(
for
(
f
<-
qscript
.
functions
if
f
.
isInstanceOf
[
BiopetCommandLineFunction
])
yield
{
def
fetchVersion
(
f
:
QFunction
)
:
Option
[(
String
,
Any
)]
=
{
f
match
{
case
f
:
BiopetJavaCommandLineFunction
with
Version
=>
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
Some
(
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
"java_md5"
->
BiopetCommandLineFunction
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
),
"java_version"
->
f
.
getJavaVersion
,
"jar_path"
->
f
.
jarFile
)
"jar_path"
->
f
.
jarFile
)
)
case
f
:
BiopetCommandLineFunction
with
Version
=>
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
Some
(
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
"md5"
->
BiopetCommandLineFunction
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
),
"path"
->
f
.
executable
)
"path"
->
f
.
executable
)
)
case
f
:
Configurable
with
Version
=>
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
))
case
_
=>
throw
new
IllegalStateException
(
"This should not be possible"
)
Some
(
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
))
)
case
_
=>
None
}
}
}).
toMap
(
qscript
.
functions
.
flatMap
(
fetchVersion
(
_
))
++
qscript
.
functions
.
flatMap
{
case
f
:
BiopetCommandLineFunction
=>
f
.
pipesJobs
}
.
flatMap
(
fetchVersion
(
_
))
).
toMap
}
val
map
=
Map
(
qscript
.
summaryName
->
((
if
(
settings
.
isEmpty
)
Map
[
String
,
Any
]()
else
Map
(
"settings"
->
settings
))
++
...
...
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