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Commit b0cd998e authored by Peter van 't Hof's avatar Peter van 't Hof
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Changed referenceFile to reference

parent 15a605f9
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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": {
}
},
"referenceFile" : "/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 referenceFile: 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)
referenceFile = config("referenceFile")
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 = referenceFile
this.reference_sequence = reference
this.memoryLimit = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
......
gatk/gatk-pipeline/examples/test.json
View file @ b0cd998e
{
"referenceFile" : "/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": {
}
},
"referenceFile" : "/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 -outputDir /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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /home/pjvan_thof/pipelines/biopet/gatk/gatk-pipeline/examples/test.json -outputDir /home/pjvan_thof/pipelines/test -l debug</exec.args>
<exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${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 -outputDir /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 referenceFile: 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)
referenceFile = 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 = referenceFile
this.reference_sequence = reference
this.memoryLimit = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
......
mapping/examples/test.json
View file @ b0cd998e
{
"samtools": {"exe": "test"},
"referenceFile": "/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":"test"}
},
"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/cutadapt"},
"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 referenceFile: File = config("referenceFile", 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(referenceFile) +
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 referenceFile: File = new File(config("referenceFile"))
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", referenceFile.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", referenceFile)
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 referenceFile: 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 (referenceFile == null) referenceFile = config("referenceFile")
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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