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biopet.biopet
Commits
8e414bb6
Commit
8e414bb6
authored
May 28, 2017
by
Peter van 't Hof
Browse files
Fixing some arguments
parent
0ace30b9
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
8e414bb6
...
...
@@ -17,9 +17,11 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
scala.util.matching.Regex
/**
* Extension for STAR
*/
...
...
@@ -28,7 +30,7 @@ class Star(val parent: Configurable)
with
Reference
with
Version
{
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
false
)
var
reference
:
File
=
null
var
reference
:
File
=
_
@Input
(
doc
=
"Fastq file R1"
,
required
=
false
)
var
R1
:
File
=
_
...
...
@@ -56,13 +58,13 @@ class Star(val parent: Configurable)
executable
=
config
(
"exe"
,
"STAR"
)
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""(.*)"""
.
r
def
versionCommand
:
String
=
executable
+
" --version"
def
versionRegex
:
Regex
=
"""(.*)"""
.
r
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
File
=
_
var
genomeDir
:
File
=
null
var
genomeDir
:
File
=
_
var
runmode
:
String
=
_
var
outFileNamePrefix
:
String
=
_
var
runThreadN
:
Option
[
Int
]
=
config
(
"runthreadn"
)
...
...
@@ -75,7 +77,7 @@ class Star(val parent: Configurable)
/** can be a list of strings **/
var
genomeChrBinNbits
:
Option
[
Int
]
=
config
(
"genomechrbinnbits"
)
var
genomeSAindexNbases
:
Option
[
Int
]
=
config
(
"genomesaindexnbases"
)
var
genomeSAindexNbases
:
Option
[
Long
]
=
config
(
"genomesaindexnbases"
)
var
genomeSAsparseD
:
Option
[
Int
]
=
config
(
"genomesasparsed"
)
@Input
(
required
=
false
)
...
...
@@ -97,12 +99,12 @@ class Star(val parent: Configurable)
var
clip3pAdapterSeq
:
Option
[
String
]
=
config
(
"clip3adapterseq"
)
var
clip3pAdapterMMp
:
Option
[
String
]
=
config
(
"clip3adaptermmp"
)
var
clip3pAfterAdapterNbases
:
Option
[
Int
]
=
config
(
"clip3afteradapternbases"
)
var
limitGenomeGenerateRAM
:
Option
[
Int
]
=
config
(
"limitgenomegenerateram"
)
var
limitIObufferSize
:
Option
[
Int
]
=
config
(
"limitiobuffersize"
)
var
limitOutSAMoneReadBytes
:
Option
[
Int
]
=
config
(
"limitoutsamonereadbytes"
)
var
limitGenomeGenerateRAM
:
Option
[
Long
]
=
config
(
"limitgenomegenerateram"
)
var
limitIObufferSize
:
Option
[
Long
]
=
config
(
"limitiobuffersize"
)
var
limitOutSAMoneReadBytes
:
Option
[
Long
]
=
config
(
"limitoutsamonereadbytes"
)
var
limitOutSJoneRead
:
Option
[
Int
]
=
config
(
"limitoutsjoneread"
)
var
limitOutSJcollapsed
:
Option
[
Int
]
=
config
(
"limitoutsjcollapsed"
)
var
limitBAMsortRAM
:
Option
[
Int
]
=
config
(
"limitbamsortram"
)
var
limitBAMsortRAM
:
Option
[
Long
]
=
config
(
"limitbamsortram"
)
var
limitSjdbInsertNsj
:
Option
[
Int
]
=
config
(
"limitsjdbinsertnsj"
)
var
outTmpDir
:
Option
[
String
]
=
config
(
"outtmpdir"
)
...
...
@@ -236,7 +238,7 @@ class Star(val parent: Configurable)
}
/** Returns command to execute */
def
cmdLine
=
{
def
cmdLine
:
String
=
{
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
" && "
+
required
(
executable
)
if
(
runmode
!=
null
&&
runmode
==
"genomeGenerate"
)
{
// Create index
cmd
+=
required
(
"--runMode"
,
runmode
)
+
...
...
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
8e414bb6
...
...
@@ -49,7 +49,7 @@ class Toucan(val parent: Configurable)
@Input
(
doc
=
"Input GVCF file"
,
shortName
=
"gvcf"
,
required
=
false
)
var
inputGvcf
:
Option
[
File
]
=
None
def
outputName
=
inputVcf
.
getName
.
stripSuffix
(
".vcf.gz"
)
def
outputName
:
String
=
inputVcf
.
getName
.
stripSuffix
(
".vcf.gz"
)
def
outputVcf
:
File
=
(
gonlVcfFile
,
exacVcfFile
)
match
{
case
(
Some
(
_
),
Some
(
_
))
=>
new
File
(
outputDir
,
s
"$outputName.vep.normalized.gonl.exac.vcf.gz"
)
...
...
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