Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
aeb3c024
Commit
aeb3c024
authored
Jan 27, 2015
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Remove outputDir from arguments
parent
c05ab685
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
3 additions
and
3 deletions
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+3
-3
No files found.
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
aeb3c024
...
...
@@ -29,11 +29,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
@Argument
(
doc
=
"JSON config file(s)"
,
fullName
=
"config_file"
,
shortName
=
"config"
,
required
=
false
)
val
configfiles
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Output directory"
,
fullName
=
"output_directory"
,
shortName
=
"outDir"
,
required
=
true
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
var
disableScatter
Default
:
Boolean
=
false
var
disableScatter
:
Boolean
=
false
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
@@ -45,11 +44,12 @@ trait BiopetQScript extends Configurable with GatkLogging {
var
functions
:
Seq
[
QFunction
]
final
def
script
()
{
outputDir
=
config
(
"output_dir"
,
required
=
true
)
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
init
biopetScript
if
(
disableScatter
Default
)
for
(
function
<-
functions
)
function
match
{
if
(
disableScatter
)
for
(
function
<-
functions
)
function
match
{
case
f
:
ScatterGatherableFunction
=>
f
.
scatterCount
=
1
case
_
=>
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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