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Mirrors
biopet.biopet
Commits
6645de03
Commit
6645de03
authored
Jul 06, 2015
by
Peter van 't Hof
Browse files
Change vals to defs
parent
30ddf578
Changes
69
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 @
6645de03
...
...
@@ -15,15 +15,15 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
jarFile
=
config
(
"gatk_jar"
)
override
val
defaultCoreMemory
=
4.0
override
def
defaultCoreMemory
=
4.0
if
(
config
.
contains
(
"intervals"
))
intervals
=
config
(
"intervals"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
))
excludeIntervals
=
config
(
"exclude_intervals"
).
asFileList
if
(
config
.
contains
(
"gatk_key"
))
gatk_key
=
config
(
"gatk_key"
)
if
(
config
.
contains
(
"pedigree"
))
pedigree
=
config
(
"pedigree"
)
override
val
versionRegex
=
"""(.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionRegex
=
"""(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" -jar "
+
jarFile
+
" -version"
override
def
getVersion
=
super
.
getVersion
.
collect
{
case
version
=>
"Gatk "
+
version
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
6645de03
...
...
@@ -33,11 +33,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
var
deps
:
List
[
File
]
=
Nil
var
threads
=
0
val
defaultThreads
=
1
def
defaultThreads
=
1
var
vmem
:
Option
[
String
]
=
config
(
"vmem"
)
protected
val
defaultCoreMemory
:
Double
=
1.0
protected
val
defaultVmemFactor
:
Double
=
1.4
protected
def
defaultCoreMemory
:
Double
=
1.0
protected
def
defaultVmemFactor
:
Double
=
1.4
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
defaultVmemFactor
)
var
residentFactor
:
Double
=
config
(
"resident_factor"
,
default
=
1.2
)
...
...
@@ -151,10 +151,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected
def
versionCommand
:
String
=
null
/** Regex to get version from version command output */
protected
val
versionRegex
:
Regex
=
null
protected
def
versionRegex
:
Regex
=
null
/** Allowed exit codes for the version command */
protected
val
versionExitcode
=
List
(
0
)
protected
def
versionExitcode
=
List
(
0
)
/** Executes the version command */
private
[
core
]
def
getVersionInternal
()
:
Option
[
String
]
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
6645de03
...
...
@@ -25,7 +25,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit
=
config
(
"java_gc_heap_freelimit"
)
javaGCTimeLimit
=
config
(
"java_gc_timelimit"
)
override
protected
val
defaultVmemFactor
:
Double
=
2.0
override
protected
def
defaultVmemFactor
:
Double
=
2.0
/** Constructs java opts, this adds scala threads */
override
def
javaOpts
=
super
.
javaOpts
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
6645de03
...
...
@@ -26,7 +26,7 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
/** Arguments that are passed on the commandline */
var
args
:
Map
[
String
,
String
]
=
Map
()
override
val
defaultCoreMemory
=
3.0
override
def
defaultCoreMemory
=
3.0
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
6645de03
...
...
@@ -40,12 +40,12 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
var
output
:
File
=
null
executable
=
config
(
"exe"
,
default
=
"bowtie"
,
freeVar
=
false
)
override
val
versionRegex
=
""".*[Vv]ersion:? (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionRegex
=
""".*[Vv]ersion:? (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" --version"
override
val
defaultCoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
defaultCoreMemory
=
4.0
override
def
defaultThreads
=
8
var
sam
:
Boolean
=
config
(
"sam"
,
default
=
true
)
var
sam_RG
:
Option
[
String
]
=
config
(
"sam-RG"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
View file @
6645de03
...
...
@@ -30,10 +30,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"cufflinks"
)
/** default threads */
override
val
defaultThreads
=
8
override
def
defaultThreads
=
8
/** default vmem for cluster jobs */
override
val
defaultCoreMemory
=
6.0
override
def
defaultCoreMemory
=
6.0
/** input file */
@Input
(
doc
=
"Input file (SAM or BAM)"
,
required
=
true
)
...
...
@@ -184,9 +184,9 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
/** do not contact server to check for update availability [FALSE] */
var
no_update_check
:
Boolean
=
config
(
"no_update_check"
,
default
=
false
)
override
val
versionRegex
=
"""cufflinks v(.*)"""
.
r
override
def
versionRegex
=
"""cufflinks v(.*)"""
.
r
override
def
versionCommand
=
executable
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionExitcode
=
List
(
0
,
1
)
def
cmdLine
=
required
(
executable
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
View file @
6645de03
...
...
@@ -117,9 +117,9 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
/** Disable SCV correction */
var
no_scv_correction
:
Boolean
=
config
(
"no_scv_correction"
,
default
=
false
)
override
val
versionRegex
=
"""cuffquant v(.*)"""
.
r
override
def
versionRegex
=
"""cuffquant v(.*)"""
.
r
override
def
versionCommand
=
executable
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionExitcode
=
List
(
0
,
1
)
def
cmdLine
=
required
(
executable
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
6645de03
...
...
@@ -40,7 +40,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
executable
=
config
(
"exe"
,
default
=
"cutadapt"
)
override
def
versionCommand
=
executable
+
" --version"
override
val
versionRegex
=
"""(.*)"""
.
r
override
def
versionRegex
=
"""(.*)"""
.
r
var
default_clip_mode
:
String
=
config
(
"default_clip_mode"
,
default
=
"3"
)
var
opt_adapter
:
Set
[
String
]
=
config
(
"adapter"
,
default
=
Nil
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
View file @
6645de03
...
...
@@ -48,9 +48,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
var
nogroup
:
Boolean
=
config
(
"nogroup"
,
default
=
false
)
var
extract
:
Boolean
=
config
(
"extract"
,
default
=
true
)
override
val
versionRegex
=
"""FastQC (.*)"""
.
r
override
def
versionRegex
=
"""FastQC (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
val
defaultThreads
=
4
override
def
defaultThreads
=
4
/** Sets contaminants and adapters when not yet set */
override
def
beforeGraph
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
6645de03
...
...
@@ -39,7 +39,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var
haplotypeLength
:
Option
[
Int
]
=
config
(
"haplotype_length"
)
executable
=
config
(
"exe"
,
default
=
"freebayes"
)
override
val
versionRegex
=
"""version: (.*)"""
.
r
override
def
versionRegex
=
"""version: (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeGraph
:
Unit
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
View file @
6645de03
...
...
@@ -32,10 +32,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
executable
=
config
(
"exe"
,
default
=
"gsnap"
,
freeVar
=
false
)
/** default threads */
override
val
defaultThreads
=
8
override
def
defaultThreads
=
8
/** default vmem for cluster jobs */
override
val
defaultCoreMemory
=
10.0
override
def
defaultCoreMemory
=
10.0
/** input file */
@Input
(
doc
=
"Input FASTQ file(s)"
,
required
=
true
)
//var input: List[File] = _
...
...
@@ -329,7 +329,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
/** value to put into read-group library (rg-pl) field */
var
read_group_platform
:
Option
[
String
]
=
config
(
"read_group_platform"
)
override
val
versionRegex
=
""".* version (.*)"""
.
r
override
def
versionRegex
=
""".* version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
def
cmdLine
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
View file @
6645de03
...
...
@@ -29,7 +29,7 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"gzip"
)
override
val
versionRegex
=
"""gzip (.*)"""
.
r
override
def
versionRegex
=
"""gzip (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
def
cmdLine
=
required
(
executable
)
+
" -c "
+
repeat
(
input
)
+
" > "
+
required
(
output
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
View file @
6645de03
...
...
@@ -69,7 +69,7 @@ class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction {
/** suppress progress report */
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
override
val
versionRegex
=
""".*, version (.*)\."""
.
r
override
def
versionRegex
=
""".*, version (.*)\."""
.
r
override
def
versionCommand
=
executable
+
" --help"
def
cmdLine
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
View file @
6645de03
...
...
@@ -33,7 +33,7 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"md5sum"
)
override
val
versionRegex
=
"""md5sum \(GNU coreutils\) (.*)"""
.
r
override
def
versionRegex
=
"""md5sum \(GNU coreutils\) (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
/** return commandline to execute */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
View file @
6645de03
...
...
@@ -33,8 +33,8 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
var
decomrpess
=
true
var
memory
:
Option
[
Int
]
=
config
(
"memory"
)
override
val
defaultCoreMemory
=
memory
.
getOrElse
(
1000
).
toDouble
/
1000
override
val
defaultThreads
=
2
override
def
defaultCoreMemory
=
memory
.
getOrElse
(
1000
).
toDouble
/
1000
override
def
defaultThreads
=
2
override
def
beforeCmd
{
if
(!
memory
.
isEmpty
)
memory
=
Option
(
memory
.
get
*
threads
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
View file @
6645de03
...
...
@@ -27,9 +27,9 @@ import scalaz.std.boolean.option
*/
class
Raxml
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
override
val
defaultThreads
=
1
override
def
defaultThreads
=
1
override
def
versionCommand
=
executable
+
" -v"
override
val
versionRegex
=
""".*version ([\w\.]*) .*"""
.
r
override
def
versionRegex
=
""".*version ([\w\.]*) .*"""
.
r
@Input
(
doc
=
"Input phy/fasta file"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
6645de03
...
...
@@ -58,7 +58,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
var
discardN
:
Boolean
=
config
(
"discardN"
,
default
=
false
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
var
defaultQualityType
:
String
=
config
(
"defaultqualitytype"
,
default
=
"sanger"
)
override
val
versionRegex
=
"""sickle version (.*)"""
.
r
override
def
versionRegex
=
"""sickle version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
/** Sets qualityType is still empty */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
View file @
6645de03
...
...
@@ -60,12 +60,12 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Refe
var
logfile
:
Option
[
String
]
=
config
(
"logfile"
)
executable
=
config
(
"exe"
,
default
=
"stampy.py"
,
freeVar
=
false
)
override
val
versionRegex
=
"""stampy v(.*) \(.*\), .*"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionRegex
=
"""stampy v(.*) \(.*\), .*"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
/// Stampy uses approx factor 1.1 times the size of the genome in memory.
override
val
defaultCoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
defaultCoreMemory
=
4.0
override
def
defaultThreads
=
8
override
def
versionCommand
=
executable
+
" --help"
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
6645de03
...
...
@@ -63,8 +63,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
var
outFileNamePrefix
:
String
=
_
var
runThreadN
:
Option
[
Int
]
=
config
(
"runThreadN"
)
override
val
defaultCoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
defaultCoreMemory
=
4.0
override
def
defaultThreads
=
8
/** Sets output files for the graph */
override
def
beforeGraph
()
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
View file @
6645de03
...
...
@@ -60,8 +60,8 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"tabix"
)
override
def
versionCommand
=
executable
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionRegex
=
"""Version: (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
/** Formats that tabix can handle */
private
val
validFormats
:
Set
[
String
]
=
Set
(
"gff"
,
"bed"
,
"sam"
,
"vcf"
,
"psltbl"
)
...
...
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