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biopet.biopet
Commits
b8084935
Commit
b8084935
authored
Feb 09, 2015
by
Peter van 't Hof
Browse files
Remove required from config calls
parent
b7fe37de
Changes
16
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
View file @
b8084935
...
...
@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
override
def
subPath
=
"gatk"
::
super
.
subPath
jarFile
=
config
(
"gatk_jar"
,
required
=
true
)
jarFile
=
config
(
"gatk_jar"
)
override
val
defaultVmem
=
"7G"
if
(
config
.
contains
(
"intervals"
))
intervals
=
config
(
"intervals"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
))
excludeIntervals
=
config
(
"exclude_intervals"
).
asFileList
reference_sequence
=
config
(
"reference"
,
required
=
true
)
reference_sequence
=
config
(
"reference"
)
if
(
config
.
contains
(
"gatk_key"
))
gatk_key
=
config
(
"gatk_key"
)
if
(
config
.
contains
(
"pedigree"
))
pedigree
=
config
(
"pedigree"
).
asFileList
}
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
b8084935
...
...
@@ -35,7 +35,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var
jointGenotyping
:
Boolean
=
config
(
"joint_genotyping"
,
default
=
false
)
var
singleSampleCalling
=
config
(
"single_sample_calling"
,
default
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
var
useAllelesOption
:
Boolean
=
config
(
"use_alleles_option"
,
default
=
false
)
val
externalGvcfs
=
config
(
"external_gvcfs_files"
,
default
=
Nil
).
asFileList
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
b8084935
...
...
@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var
rawVcfInput
:
File
=
_
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Argument
(
doc
=
"OutputName"
,
required
=
false
)
var
outputName
:
String
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
b8084935
...
...
@@ -51,7 +51,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
var
functions
:
Seq
[
QFunction
]
final
def
script
()
{
outputDir
=
config
(
"output_dir"
,
required
=
true
)
outputDir
=
config
(
"output_dir"
)
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
init
biopetScript
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
b8084935
...
...
@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
View file @
b8084935
...
...
@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"ref"
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Input
(
doc
=
"The genome prefix."
)
var
genome
:
File
=
config
(
"genome"
,
required
=
true
)
var
genome
:
File
=
config
(
"genome"
)
@Input
(
doc
=
"The hash prefix"
)
var
hash
:
File
=
config
(
"hash"
,
required
=
true
)
var
hash
:
File
=
config
(
"hash"
)
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
View file @
b8084935
...
...
@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
var
R2
:
File
=
_
@Input
(
doc
=
"Bowtie index"
,
shortName
=
"bti"
)
var
bowtie_index
:
File
=
config
(
"bowtie_index"
,
required
=
true
)
var
bowtie_index
:
File
=
config
(
"bowtie_index"
)
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
String
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
View file @
b8084935
...
...
@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var
fastq
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Output
(
doc
=
"Output file SAM"
,
required
=
false
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
b8084935
...
...
@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
b8084935
...
...
@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
var
saiR2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Output
(
doc
=
"Output file SAM"
,
required
=
false
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
View file @
b8084935
...
...
@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var
sai
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Output
(
doc
=
"Output file SAM"
,
required
=
false
)
var
output
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
b8084935
...
...
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
var
outputSummary
:
File
=
_
@Argument
(
doc
=
"Reference file"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
@Argument
(
doc
=
"Window size"
,
required
=
false
)
var
windowSize
:
Option
[
Int
]
=
config
(
"windowsize"
)
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
View file @
b8084935
...
...
@@ -30,9 +30,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
@Test
def
testApply
:
Unit
=
{
ConfigTest
.
config
(
"m1"
,
Nil
,
"k1"
).
asString
shouldBe
"v2"
ConfigTest
.
config
(
"m1"
,
Nil
,
"notexist"
,
default
=
"default"
).
asString
shouldBe
"default"
intercept
[
IllegalStateException
]
{
ConfigTest
.
config
(
"m1"
,
Nil
,
"notexist"
)
}
}
@Test
def
testMergeConfigs
:
Unit
=
{
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
View file @
b8084935
...
...
@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC
.
classB
.
get
(
"k1"
).
asString
shouldBe
"c1"
classC
.
classB
.
classA
.
get
(
"k1"
).
asString
shouldBe
"c1"
classC
.
get
(
"notexist"
)
shouldBe
null
intercept
[
IllegalStateException
]
{
classC
.
get
(
"notexist"
,
required
=
true
)
}
classC
.
get
(
"notexist"
,
default
=
"default"
).
asString
shouldBe
"default"
classC
.
get
(
"k1"
,
freeVar
=
false
).
asString
shouldBe
"c1"
...
...
@@ -47,11 +43,10 @@ abstract class Cfg extends Configurable {
def
get
(
key
:
String
,
default
:
String
=
null
,
submodule
:
String
=
null
,
required
:
Boolean
=
false
,
freeVar
:
Boolean
=
true
,
sample
:
String
=
null
,
library
:
String
=
null
)
=
{
config
(
key
,
default
,
submodule
,
required
,
freeVar
=
freeVar
,
sample
=
sample
,
library
=
library
)
config
(
key
,
default
,
submodule
,
freeVar
=
freeVar
,
sample
=
sample
,
library
=
library
)
}
}
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
b8084935
...
...
@@ -60,7 +60,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
val
inputFastq
:
File
=
config
(
"R1"
,
required
=
true
)
val
inputFastq
:
File
=
config
(
"R1"
)
val
prefixFastq
:
File
=
createFile
(
".prefix.fastq"
)
val
flexiprep
=
new
Flexiprep
(
qscript
)
...
...
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
b8084935
...
...
@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class
Yamsvp
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
//with MultiSampleQScript {
def
this
()
=
this
(
null
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
var
finalBamFiles
:
List
[
File
]
=
Nil
/*
class LibraryOutput extends AbstractLibraryOutput {
...
...
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