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
5b09944b
Commit
5b09944b
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Fixed reference and added version
parent
b80652eb
Changes
1
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CommandLineGATK.scala
View file @
5b09944b
...
...
@@ -2,11 +2,11 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Input
,
Output
,
Argument
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
trait
CommandLineGATK
extends
BiopetJavaCommandLineFunction
{
trait
CommandLineGATK
extends
BiopetJavaCommandLineFunction
with
Reference
with
Version
{
analysisName
=
"CommandLineGATK"
javaMainClass
=
"org.broadinstitute.gatk.engine.CommandLineGATK"
jarFile
=
config
(
"gatk_jar"
)
...
...
@@ -316,8 +316,13 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction {
@Argument
(
fullName
=
"version"
,
shortName
=
"version"
,
doc
=
"Output version information"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
var
version
:
Boolean
=
_
override
def
freezeFieldValues
()
{
super
.
freezeFieldValues
()
def
versionRegex
=
"""(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
executable
+
" -jar "
+
jarFile
+
" -version"
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference_sequence
!=
null
)
reference_sequence
=
referenceFasta
()
input_fileIndexes
++=
input_file
.
filter
(
orig
=>
orig
!=
null
&&
orig
.
getName
.
endsWith
(
".bam"
)).
flatMap
(
orig
=>
Array
(
new
File
(
orig
.
getPath
+
".bai"
),
new
File
(
orig
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
)))
if
(
num_threads
.
isDefined
)
nCoresRequest
=
num_threads
if
(
num_cpu_threads_per_data_thread
.
isDefined
)
nCoresRequest
=
Some
(
nCoresRequest
.
getOrElse
(
1
)
*
num_cpu_threads_per_data_thread
.
getOrElse
(
1
))
...
...
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