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biopet.biopet
Commits
f4d7e851
Commit
f4d7e851
authored
Mar 19, 2015
by
bow
Browse files
Fix incorrectly passed java flags for piped VarScan command
parent
5bd4ef22
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
View file @
f4d7e851
...
...
@@ -63,20 +63,27 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
override
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"-vP"
)
+
required
(
"""\t\t"""
)
}
private
def
varscan
=
new
Mpileup2cns
(
wrapper
.
root
)
{
private
val
varscan
=
new
Mpileup2cns
(
wrapper
.
root
)
{
strandFilter
=
Option
(
0
)
outputVcf
=
Option
(
1
)
}
private
def
compress
=
new
Bgzip
(
wrapper
.
root
)
{
this
.
output
=
wrapper
.
output
}
private
val
compress
=
new
Bgzip
(
wrapper
.
root
)
private
def
index
=
new
Tabix
(
wrapper
.
root
)
{
private
val
index
=
new
Tabix
(
wrapper
.
root
)
{
input
=
compress
.
output
p
=
Option
(
"vcf"
)
}
override
def
freezeFieldValues
()
:
Unit
=
{
varscan
.
output
=
Option
(
new
File
(
wrapper
.
output
.
toString
.
stripSuffix
(
".gz"
)))
compress
.
input
=
List
(
varscan
.
output
.
get
)
compress
.
output
=
this
.
output
super
.
freezeFieldValues
()
varscan
.
qSettings
=
this
.
qSettings
varscan
.
freezeFieldValues
()
}
override
def
beforeGraph
:
Unit
=
{
require
(
output
.
toString
.
endsWith
(
".gz"
),
"Output must have a .gz file extension"
)
}
...
...
@@ -85,6 +92,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// FIXME: manual trigger of commandLine for version retrieval
mpileup
.
commandLine
mpileup
.
cmdPipe
+
" | "
+
fixMpileup
.
commandLine
+
" | "
+
removeEmptyPile
.
commandLine
+
" | "
+
varscan
.
commandLine
+
"
|
"
+
compress
.
commandLine
+
" && "
+
index
.
commandLine
varscan
.
commandLine
+
"
&&
"
+
compress
.
commandLine
+
" && "
+
index
.
commandLine
}
}
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