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
92dc5c59
Commit
92dc5c59
authored
Nov 05, 2014
by
Peter van 't Hof
Browse files
Removed config file reading, already done in biopetQScript
parent
d2f9c54e
Changes
5
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
92dc5c59
...
...
@@ -26,7 +26,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
var
wholeGenome
=
false
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on BamMetrics module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
if
(
config
.
contains
(
"target_bed"
))
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
92dc5c59
...
...
@@ -43,7 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
summary
=
new
FlexiprepSummary
(
this
)
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
if
(!
skipTrim
)
skipTrim
=
config
(
"skiptrim"
,
default
=
false
)
if
(!
skipClip
)
skipClip
=
config
(
"skipclip"
,
default
=
false
)
if
(
input_R1
==
null
)
throw
new
IllegalStateException
(
"Missing R1 on flexiprep module"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
92dc5c59
...
...
@@ -69,7 +69,7 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
var
cExonBase
:
Boolean
=
_
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
}
def
biopetScript
()
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
92dc5c59
...
...
@@ -81,7 +81,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
val
flexiprep
=
new
Flexiprep
(
this
)
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
if
(
aligner
==
null
)
aligner
=
config
(
"aligner"
,
default
=
defaultAligner
)
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on mapping module"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
92dc5c59
...
...
@@ -34,7 +34,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
}
override
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
reference
=
config
(
"reference"
,
required
=
true
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Output directory is not specified in the config / argument"
)
...
...
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