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biopet.biopet
Commits
b0cd998e
Commit
b0cd998e
authored
Aug 11, 2014
by
Peter van 't Hof
Browse files
Changed referenceFile to reference
parent
15a605f9
Changes
11
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Inline
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flexiprep/nbactions.xml
View file @
b0cd998e
...
...
@@ -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 -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
run
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
sample test -library test
</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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
run
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
sample test -library test
</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 -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
run
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -R2 /media/LocalData/test/1k_R2_001.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -
sample test -library test
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
gatk/gatk-old/examples/test.json
View file @
b0cd998e
...
...
@@ -14,7 +14,7 @@
"flexiprep"
:
{
}
},
"reference
File
"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"reference"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"dbsnp"
:
"test"
,
"hapmap"
:
"test"
,
"omni"
:
"test"
,
...
...
gatk/gatk-old/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
View file @
b0cd998e
...
...
@@ -22,14 +22,14 @@ class Gatk(val root: Configurable) extends QScript with MultiSampleQScript {
@Argument
(
doc
=
"Only Sample"
,
shortName
=
"sample"
,
required
=
false
)
val
onlySample
:
String
=
""
var
reference
File
:
File
=
_
var
reference
:
File
=
_
var
dbsnp
:
File
=
_
var
gvcfFiles
:
List
[
File
]
=
Nil
var
finalBamFiles
:
List
[
File
]
=
Nil
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
reference
File
=
config
(
"reference
File
"
)
reference
=
config
(
"reference"
)
if
(
configContains
(
"dbsnp"
))
dbsnp
=
config
(
"dbsnp"
)
for
(
file
<-
config
(
"gvcfFiles"
,
Nil
).
getList
)
gvcfFiles
:+=
file
.
toString
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on gatk module"
)
...
...
@@ -286,7 +286,7 @@ class Gatk(val root: Configurable) extends QScript with MultiSampleQScript {
}
trait
gatkArguments
extends
CommandLineGATK
{
this
.
reference_sequence
=
reference
File
this
.
reference_sequence
=
reference
this
.
memoryLimit
=
2
this
.
jobResourceRequests
:+=
"h_vmem=4G"
}
...
...
gatk/gatk-pipeline/examples/test.json
View file @
b0cd998e
{
"reference
File
"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"reference"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"reference"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"samtools"
:
{
"exe"
:
"test"
},
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
...
...
@@ -15,7 +15,7 @@
"flexiprep"
:
{
}
},
"reference
File
"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"reference"
:
"/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta"
,
"dbsnp"
:
"test"
,
"hapmap"
:
"test"
,
"omni"
:
"test"
,
...
...
gatk/gatk-pipeline/nbactions.xml
View file @
b0cd998e
...
...
@@ -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.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -out
put
Dir /home/pjvan_thof/pipelines/test -l debug
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -outDir /home/pjvan_thof/pipelines/test -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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -out
put
Dir /home/pjvan_thof/pipelines/test -l debug
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -outDir /home/pjvan_thof/pipelines/test -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.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -out
put
Dir /home/pjvan_thof/pipelines/test -l debug
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -outDir /home/pjvan_thof/pipelines/test -l debug
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
b0cd998e
...
...
@@ -22,14 +22,14 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
@Argument
(
doc
=
"Merge gvcfs"
,
shortName
=
"mergegvcfs"
,
required
=
false
)
var
mergeGvcfs
:
Boolean
=
false
var
reference
File
:
File
=
_
var
reference
:
File
=
_
var
dbsnp
:
File
=
_
var
gvcfFiles
:
List
[
File
]
=
Nil
var
finalBamFiles
:
List
[
File
]
=
Nil
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
reference
File
=
config
(
"reference"
,
required
=
true
)
reference
=
config
(
"reference"
,
required
=
true
)
dbsnp
=
config
(
"dbsnp"
)
if
(
configContains
(
"gvcfFiles"
))
for
(
file
<-
config
(
"gvcfFiles"
).
getList
)
...
...
@@ -224,7 +224,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
trait
gatkArguments
extends
CommandLineGATK
{
this
.
reference_sequence
=
reference
File
this
.
reference_sequence
=
reference
this
.
memoryLimit
=
2
this
.
jobResourceRequests
:+=
"h_vmem=4G"
}
...
...
mapping/examples/test.json
View file @
b0cd998e
{
"samtools"
:
{
"exe"
:
"test"
},
"reference
File
"
:
"/blabla/blabla.fa"
,
"reference"
:
"/blabla/blabla.fa"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"bwa"
:
{
"exe"
:
"test"
},
"flexiprep"
:
{
"fastqc"
:
{
"exe"
:
"test"
},
"
cutadapt
"
:
{
"exe"
:
"
test
"
},
"
sickle
"
:
{
"exe"
:
"
tes
t"
}
}
,
"chunking"
:
false
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"
seqtk
"
:
{
"exe"
:
"
/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk
"
},
"
cutadapt
"
:
{
"exe"
:
"
/home/pjvan_thof/.local/bin/cutadap
t"
}
,
"sickle"
:
{
"exe"
:
"/data/DIV5/SASC/pjvan_thof/bin/sickle"
}
}
}
mapping/nbactions.xml
View file @
b0cd998e
...
...
@@ -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 -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.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
-numberChunks 10
</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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${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
-numberChunks 10
</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 -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.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
-numberChunks 10
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
View file @
b0cd998e
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.aligners
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
import
scala.sys.process._
...
...
@@ -14,7 +14,7 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
File
:
File
=
config
(
"reference
File
"
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
@@ -37,7 +37,7 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
optional
(
"-t"
,
nCoresRequest
)
+
optional
(
"-R"
,
RG
)
+
conditional
(
M
,
"-M"
)
+
required
(
reference
File
)
+
required
(
reference
)
+
required
(
R1
)
+
optional
(
R2
)
+
" > "
+
required
(
output
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala
View file @
b0cd998e
...
...
@@ -8,7 +8,7 @@ import scala.sys.process._
class
Star
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
false
)
var
reference
File
:
File
=
new
File
(
config
(
"reference
File
"
))
var
reference
:
File
=
new
File
(
config
(
"reference"
))
@Input
(
doc
=
"Fastq file R1"
,
required
=
false
)
var
R1
:
File
=
_
...
...
@@ -39,7 +39,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
String
=
_
var
genomeDir
:
String
=
config
(
"genomeDir"
,
reference
File
.
getParent
+
"/star/"
)
var
genomeDir
:
String
=
config
(
"genomeDir"
,
reference
.
getParent
+
"/star/"
)
var
runmode
:
String
=
_
var
sjdbOverhang
:
Int
=
_
var
outFileNamePrefix
:
String
=
_
...
...
@@ -67,7 +67,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"&&"
+
required
(
executable
)
if
(
runmode
!=
null
&&
runmode
==
"genomeGenerate"
)
{
// Create index
cmd
+=
required
(
"--runMode"
,
runmode
)
+
required
(
"--genomeFastaFiles"
,
reference
File
)
required
(
"--genomeFastaFiles"
,
reference
)
}
else
{
// Aligner
cmd
+=
required
(
"--readFilesIn"
,
R1
)
+
optional
(
R2
)
}
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
b0cd998e
...
...
@@ -37,7 +37,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
aligner
:
String
=
_
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
File
:
File
=
_
var
reference
:
File
=
_
@Argument
(
doc
=
"Chunking"
,
shortName
=
"chunking"
,
required
=
false
)
var
chunking
:
Boolean
=
false
...
...
@@ -83,7 +83,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if
(
inputtype
==
"rna"
)
aligner
=
config
(
"aligner"
,
"star-2pass"
)
else
aligner
=
config
(
"aligner"
,
"bwa"
)
}
if
(
reference
File
==
null
)
reference
File
=
config
(
"reference
File
"
)
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on mapping module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
if
(
input_R1
==
null
)
throw
new
IllegalStateException
(
"Missing Fastq R1 on mapping module"
)
...
...
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