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Mirrors
biopet.biopet
Commits
6b5c4320
Commit
6b5c4320
authored
Jul 30, 2014
by
Peter van 't Hof
Browse files
Wrappers are now split in general and specific flexiprep extensions
parent
a2275bd4
Changes
11
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
0 → 100644
View file @
6b5c4320
package
nl.lumc.sasc.biopet.extensions
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
class
Cutadapt
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Input fastq file"
)
var
fastq_input
:
File
=
_
@Output
(
doc
=
"Output fastq file"
)
var
fastq_output
:
File
=
_
@Output
(
doc
=
"Output statistics file"
)
var
stats_output
:
File
=
_
executable
=
config
(
"exe"
,
default
=
"cutadapt"
)
override
def
versionCommand
=
executable
+
" --version"
override
val
versionRegex
=
"""(.*)"""
.
r
var
default_clip_mode
:
String
=
config
(
"default_clip_mode"
,
default
=
"3"
)
var
opt_adapter
:
Set
[
String
]
=
Set
()
+
config
(
"adapter"
)
var
opt_anywhere
:
Set
[
String
]
=
Set
()
+
config
(
"anywhere"
)
var
opt_front
:
Set
[
String
]
=
Set
()
+
config
(
"front"
)
var
opt_discard
:
Boolean
=
config
(
"discard"
)
var
opt_minimum_length
:
String
=
config
(
"minimum_length"
,
1
)
var
opt_maximum_length
:
String
=
config
(
"maximum_length"
)
def
cmdLine
=
required
(
executable
)
+
// options
repeat
(
"-a"
,
opt_adapter
)
+
repeat
(
"-b"
,
opt_anywhere
)
+
repeat
(
"-g"
,
opt_front
)
+
conditional
(
opt_discard
,
"--discard"
)
+
optional
(
"-m"
,
opt_minimum_length
)
+
optional
(
"-M"
,
opt_maximum_length
)
+
// input / output
required
(
fastq_input
)
+
required
(
"--output"
,
fastq_output
)
+
" > "
+
required
(
stats_output
)
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
0 → 100644
View file @
6b5c4320
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
class
Fastqc
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Contaminants"
,
required
=
false
)
var
contaminants
:
File
=
_
@Input
(
doc
=
"Fastq file"
,
shortName
=
"FQ"
)
var
fastqfile
:
File
=
_
@Output
(
doc
=
"Output"
,
shortName
=
"out"
)
var
output
:
File
=
_
executable
=
config
(
"exe"
,
default
=
"fastqc"
)
var
java_exe
:
String
=
config
(
"exe"
,
default
=
"java"
,
submodule
=
"java"
)
var
kmers
:
Option
[
Int
]
=
config
(
"kmers"
)
var
quiet
:
Boolean
=
config
(
"quiet"
)
var
noextract
:
Boolean
=
config
(
"noextract"
)
var
nogroup
:
Boolean
=
config
(
"nogroup"
)
var
extract
:
Boolean
=
config
(
"extract"
,
default
=
true
)
override
val
versionRegex
=
"""FastQC (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
val
defaultThreads
=
4
override
def
afterGraph
{
this
.
checkExecutable
if
(
contaminants
==
null
)
{
val
fastqcDir
=
executable
.
substring
(
0
,
executable
.
lastIndexOf
(
"/"
))
contaminants
=
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
}
}
def
cmdLine
=
required
(
executable
)
+
optional
(
"--java"
,
java_exe
)
+
optional
(
"--threads"
,
threads
)
+
optional
(
"--contaminants"
,
contaminants
)
+
optional
(
"--kmers"
,
kmers
)
+
conditional
(
nogroup
,
"--nogroup"
)
+
conditional
(
noextract
,
"--noextract"
)
+
conditional
(
extract
,
"--extract"
)
+
conditional
(
quiet
,
"--quiet"
)
+
required
(
"-o"
,
output
.
getParent
())
+
required
(
fastqfile
)
}
flexiprep
/src/main/scala/nl/lumc/sasc/biopet/extensions/
fastq/
Sickle.scala
→
biopet-framework
/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
6b5c4320
package
nl.lumc.sasc.biopet.extensions
.fastq
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
scala.io.Source._
import
scala.sys.process._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
Sickle
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"R1 input"
)
...
...
@@ -19,9 +13,6 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
@Input
(
doc
=
"R2 input"
,
required
=
false
)
var
input_R2
:
File
=
_
@Input
(
doc
=
"qualityType file"
,
required
=
false
)
var
qualityTypeFile
:
File
=
_
@Output
(
doc
=
"R1 output"
)
var
output_R1
:
File
=
_
...
...
@@ -41,17 +32,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var
defaultQualityType
:
String
=
config
(
"defaultqualitytype"
,
default
=
"sanger"
)
override
val
versionRegex
=
"""sickle version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
def
afterGraph
{
if
(
qualityType
==
null
&&
defaultQualityType
!=
null
)
qualityType
=
defaultQualityType
}
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeCmd
{
qualityType
=
getQualityTypeFromFile
}
def
cmdLine
=
{
var
cmd
:
String
=
required
(
executable
)
if
(
input_R2
!=
null
)
{
...
...
@@ -67,26 +53,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
required
(
"-o"
,
output_R1
)
+
" > "
+
required
(
output_stats
)
}
def
getQualityTypeFromFile
:
String
=
{
if
(
qualityType
==
null
&&
qualityTypeFile
!=
null
)
{
if
(
qualityTypeFile
.
exists
())
{
for
(
line
<-
fromFile
(
qualityTypeFile
).
getLines
)
{
var
s
:
String
=
line
.
substring
(
0
,
line
.
lastIndexOf
(
"\t"
))
return
s
}
}
else
logger
.
warn
(
"File : "
+
qualityTypeFile
+
" does not exist"
)
}
return
null
}
def
getSummary
:
Json
=
{
return
jNull
}
}
object
Sickle
{
def
mergeSummarys
(
jsons
:
List
[
Json
])
:
Json
=
{
return
jNull
}
}
\ No newline at end of file
flexiprep/nbactions.xml
View file @
6b5c4320
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/
extensions/fastq
/Cutadapt.scala
→
flexiprep/src/main/scala/nl/lumc/sasc/biopet/
pipelines/flexiprep
/Cutadapt.scala
View file @
6b5c4320
package
nl.lumc.sasc.biopet.extensions.fastq
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
import
java.io.File
import
scala.io.Source._
import
scala.
sys.process._
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
scala.
io.Source
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
org.broadinstitute.gatk.utils.commandline.
{
Input
}
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.Ln
class
Cutadapt
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Input fastq file"
)
var
fastq_input
:
File
=
_
class
Cutadapt
(
root
:
Configurable
)
extends
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Cutadapt
(
root
)
{
@Input
(
doc
=
"Fastq contams file"
,
required
=
false
)
var
contams_file
:
File
=
_
@Output
(
doc
=
"Output fastq file"
)
var
fastq_output
:
File
=
_
@Output
(
doc
=
"Output statistics file"
)
var
stats_output
:
File
=
_
executable
=
config
(
"exe"
,
default
=
"cutadapt"
)
override
def
versionCommand
=
executable
+
" --version"
override
val
versionRegex
=
"""(.*)"""
.
r
var
default_clip_mode
:
String
=
config
(
"default_clip_mode"
,
default
=
"3"
)
var
opt_adapter
:
Set
[
String
]
=
Set
()
+
config
(
"adapter"
)
var
opt_anywhere
:
Set
[
String
]
=
Set
()
+
config
(
"anywhere"
)
var
opt_front
:
Set
[
String
]
=
Set
()
+
config
(
"front"
)
var
opt_discard
:
Boolean
=
config
(
"discard"
)
var
opt_minimum_length
:
String
=
config
(
"minimum_length"
,
1
)
var
opt_maximum_length
:
String
=
config
(
"maximum_length"
)
override
def
beforeCmd
()
{
super
.
beforeCmd
getContamsFromFile
}
def
cmdLine
=
{
override
def
cmdLine
=
{
if
(!
opt_adapter
.
isEmpty
||
!
opt_anywhere
.
isEmpty
||
!
opt_front
.
isEmpty
)
{
analysisName
=
getClass
.
getName
required
(
executable
)
+
// options
repeat
(
"-a"
,
opt_adapter
)
+
repeat
(
"-b"
,
opt_anywhere
)
+
repeat
(
"-g"
,
opt_front
)
+
conditional
(
opt_discard
,
"--discard"
)
+
optional
(
"-m"
,
opt_minimum_length
)
+
optional
(
"-M"
,
opt_maximum_length
)
+
// input / output
required
(
fastq_input
)
+
required
(
"--output"
,
fastq_output
)
+
" > "
+
required
(
stats_output
)
super
.
cmdLine
}
else
{
analysisName
=
getClass
.
getSimpleName
+
"-ln"
val
lnOut
=
new
Ln
(
this
)
...
...
@@ -67,11 +39,11 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
lnOut
.
cmd
}
}
def
getContamsFromFile
{
if
(
contams_file
!=
null
)
{
if
(
contams_file
.
exists
())
{
for
(
line
<-
fromFile
(
contams_file
).
getLines
)
{
for
(
line
<-
Source
.
fromFile
(
contams_file
).
getLines
)
{
var
s
:
String
=
line
.
substring
(
line
.
lastIndexOf
(
"\t"
)
+
1
,
line
.
size
)
if
(
default_clip_mode
==
"3"
)
opt_adapter
+=
s
else
if
(
default_clip_mode
==
"5"
)
opt_front
+=
s
...
...
@@ -85,7 +57,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
}
else
logger
.
warn
(
"File : "
+
contams_file
+
" does not exist"
)
}
}
def
getSummary
:
Json
=
{
return
jNull
}
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/
extensions/fastq
/Fastqc.scala
→
flexiprep/src/main/scala/nl/lumc/sasc/biopet/
pipelines/flexiprep
/Fastqc.scala
View file @
6b5c4320
package
nl.lumc.sasc.biopet.extensions.fastq
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
scala.io.Source
import
scala.sys.process._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
class
Fastqc
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Contaminants"
,
required
=
false
)
var
contaminants
:
File
=
_
@Input
(
doc
=
"Fastq file"
,
shortName
=
"FQ"
)
var
fastqfile
:
File
=
_
@Output
(
doc
=
"Output"
,
shortName
=
"out"
)
var
output
:
File
=
_
executable
=
config
(
"exe"
,
default
=
"fastqc"
)
var
java_exe
:
String
=
config
(
"exe"
,
default
=
"java"
,
submodule
=
"java"
)
var
kmers
:
Option
[
Int
]
=
config
(
"kmers"
)
var
quiet
:
Boolean
=
config
(
"quiet"
)
var
noextract
:
Boolean
=
config
(
"noextract"
)
var
nogroup
:
Boolean
=
config
(
"nogroup"
)
var
extract
:
Boolean
=
config
(
"extract"
,
default
=
true
)
override
val
versionRegex
=
"""FastQC (.*)"""
.
r
override
val
defaultThreads
=
4
override
def
afterGraph
{
this
.
checkExecutable
if
(
contaminants
==
null
)
{
val
fastqcDir
=
executable
.
substring
(
0
,
executable
.
lastIndexOf
(
"/"
))
contaminants
=
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
}
}
override
def
versionCommand
=
executable
+
" --version"
def
cmdLine
=
{
required
(
executable
)
+
optional
(
"--java"
,
java_exe
)
+
optional
(
"--threads"
,
threads
)
+
optional
(
"--contaminants"
,
contaminants
)
+
optional
(
"--kmers"
,
kmers
)
+
conditional
(
nogroup
,
"--nogroup"
)
+
conditional
(
noextract
,
"--noextract"
)
+
conditional
(
extract
,
"--extract"
)
+
conditional
(
quiet
,
"--quiet"
)
+
required
(
"-o"
,
output
.
getParent
())
+
required
(
fastqfile
)
}
class
Fastqc
(
root
:
Configurable
)
extends
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Fastqc
(
root
)
{
def
getDataBlock
(
name
:
String
)
:
Array
[
String
]
=
{
// Based on Fastqc v0.10.1
val
outputDir
=
output
.
getName
.
stripSuffix
(
".zip"
)
val
dataFile
=
new
File
(
outputDir
+
"/fastqc_data.txt"
)
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
6b5c4320
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
scala.util.parsing.json._
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk._
import
org.broadinstitute.gatk.queue.extensions.picard._
import
org.broadinstitute.gatk.queue.function._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.fastq._
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Ln
,
Pbzip2
,
Sha1sum
,
Zcat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
View file @
6b5c4320
...
...
@@ -2,10 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.Sha1sum
import
nl.lumc.sasc.biopet.extensions.fastq.Cutadapt
import
nl.lumc.sasc.biopet.extensions.fastq.Fastqc
import
nl.lumc.sasc.biopet.extensions.fastq.Sickle
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.FastqSync
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.
{
FastqSync
,
Seqstat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
0 → 100644
View file @
6b5c4320
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package
nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
scala.io.Source
import
org.broadinstitute.gatk.utils.commandline.
{
Input
}
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
class
Sickle
(
root
:
Configurable
)
extends
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Sickle
(
root
)
{
@Input
(
doc
=
"qualityType file"
,
required
=
false
)
var
qualityTypeFile
:
File
=
_
override
def
beforeCmd
{
super
.
beforeCmd
qualityType
=
getQualityTypeFromFile
}
def
getQualityTypeFromFile
:
String
=
{
if
(
qualityType
==
null
&&
qualityTypeFile
!=
null
)
{
if
(
qualityTypeFile
.
exists
())
{
for
(
line
<-
Source
.
fromFile
(
qualityTypeFile
).
getLines
)
{
var
s
:
String
=
line
.
substring
(
0
,
line
.
lastIndexOf
(
"\t"
))
return
s
}
}
else
logger
.
warn
(
"File : "
+
qualityTypeFile
+
" does not exist"
)
}
return
null
}
def
getSummary
:
Json
=
{
return
jNull
}
}
object
Sickle
{
def
mergeSummarys
(
jsons
:
List
[
Json
])
:
Json
=
{
return
jNull
}
}
\ No newline at end of file
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
View file @
6b5c4320
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import
java.io.File
import
nl.lumc.sasc.biopet.
extensions.fastq
.Fastqc
import
nl.lumc.sasc.biopet.
pipelines.flexiprep
.Fastqc
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
argonaut._
,
Argonaut
.
_
...
...
@@ -32,7 +32,6 @@ class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
case
s
if
(
s
.
contains
(
"Illumina <1.3"
))
=>
fmt
=
"solexa"
case
s
if
(
s
.
contains
(
"Illumina 1.3"
))
=>
fmt
=
"illumina"
case
s
if
(
s
.
contains
(
"Illumina 1.5"
))
=>
fmt
=
"illumina"
//case _ => null
}
}
}
...
...
mapping/nbactions.xml
View file @
6b5c4320
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -out
put
Dir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
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