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Commit 6b5c4320 authored by Peter van 't Hof's avatar Peter van 't Hof
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Wrappers are now split in general and specific flexiprep extensions

parent a2275bd4
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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 -outputDir /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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
<exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${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 -outputDir /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 -outputDir /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=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
<exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${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 -outputDir /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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