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biopet.biopet
Commits
492b52f0
Commit
492b52f0
authored
Apr 06, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 06, 2017
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Merge pull request #50 from biopet/fix-BIOPET-583
Fixing clever execution
parents
3bc12fa1
ad810026
Changes
3
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3 changed files
with
11 additions
and
10 deletions
+11
-10
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+3
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+6
-7
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+2
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
492b52f0
...
...
@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
writer
.
println
(
"set -eubf"
)
writer
.
println
(
"set -o pipefail"
)
lines
.
foreach
(
writer
.
println
)
writer
.
println
(
this
.
commandLine
)
jobDelayTime
.
foreach
(
x
=>
writer
.
println
(
s
"sleep $x"
))
writer
.
close
()
}
...
...
@@ -99,6 +99,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph
()
internalBeforeGraph
()
this
.
commandDirectory
=
this
.
jobOutputFile
.
getParentFile
super
.
freezeFieldValues
()
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
View file @
492b52f0
...
...
@@ -38,17 +38,16 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
@Input
(
doc
=
"Reference"
)
var
reference
:
File
=
_
protected
def
cleverOutputDir
:
File
=
new
File
(
cleverWorkDir
,
"work"
)
var
cleverWorkDir
:
File
=
_
@Output
(
doc
=
"Clever VCF output"
)
lazy
val
outputvcf
:
File
=
{
new
File
(
clever
Output
Dir
,
"predictions.vcf"
)
new
File
(
clever
Work
Dir
,
"predictions.vcf"
)
}
@Output
(
doc
=
"Clever raw output"
)
lazy
val
outputraw
:
File
=
{
new
File
(
clever
Output
Dir
,
"predictions.raw.txt"
)
new
File
(
clever
Work
Dir
,
"predictions.raw.txt"
)
}
// var T: Option[Int] = config("T", default = defaultThreads)
...
...
@@ -60,13 +59,13 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
clever
Output
Dir
==
null
)
throw
new
Exception
(
"Clever :: Workdirectory is not defined"
)
if
(
clever
Work
Dir
==
null
)
throw
new
Exception
(
"Clever :: Workdirectory is not defined"
)
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
def
cmdLine
=
required
(
executable
)
+
"
--sorted
"
+
"
--use_xa
"
+
required
(
"--sorted"
)
+
required
(
"--use_xa"
)
+
optional
(
"-T"
,
threads
)
+
conditional
(
f
,
"-f"
)
+
conditional
(
a
,
"-a"
)
+
...
...
@@ -74,7 +73,7 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
conditional
(
r
,
"-r"
)
+
required
(
input
)
+
required
(
reference
)
+
required
(
clever
Output
Dir
)
required
(
clever
Work
Dir
)
}
object
CleverCaller
{
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
View file @
492b52f0
...
...
@@ -23,10 +23,10 @@ class Clever(val parent: Configurable) extends SvCaller {
def
name
=
"clever"
def
biopetScript
()
{
//TODO: check double directories
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
this
,
bamFile
,
cleverDir
)
val
clever
=
CleverCaller
(
this
,
bamFile
,
new
File
(
cleverDir
,
"clever_output"
))
clever
.
jobOutputFile
=
new
File
(
cleverDir
,
".CleverCaller.out"
)
add
(
clever
)
val
cleverVCF
=
new
CleverFixVCF
(
this
)
...
...
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