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Commit bd8a2a63 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added BiopetCommandlineFunction 

All commandlinefunctions now extends from this trait
parent c4bdd49e
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 0 → 100644
View file @ bd8a2a63
package nl.lumc.sasc.biopet.core
import java.io.File
import org.broadinstitute.sting.queue.QException
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import scala.sys.process._
import scala.util.matching.Regex
trait BiopetCommandLineFunction extends CommandLineFunction {
val globalConfig: Config
analysisName = getClass.getSimpleName
protected var config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
logger.debug("config passed for " + analysisName)
@Input(doc="deps", required=false)
var deps: List[File] = Nil
@Argument(doc="Threads", required=false)
var threads = 0
val defaultThreads = 1
@Argument(doc="Vmem", required=false)
var vmem: String = _
val defaultVmem: String = ""
@Argument(doc="Executeble")
var executeble: String = _
protected def beforeCmd {
}
protected def afterGraph {
}
def setConfig(name:String) {
analysisName = name
config = Config.mergeConfigs(config.getAsConfig(analysisName.toLowerCase), config)
}
override def freezeFieldValues() {
checkExecuteble
afterGraph
jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
super.freezeFieldValues()
}
protected def checkExecuteble {
try if (executeble != null) {
val buffer = new StringBuffer()
val cmd = Seq("which", executeble)
val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
if (process.exitValue == 0) {
executeble = buffer.toString
val file = new File(executeble)
executeble = file.getCanonicalPath
} else {
logger.error("executeble: '" + executeble + "' not found, please check config")
throw new QException("executeble: '" + executeble + "' not found, please check config")
}
} catch {
case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
}
}
final protected def preCmdInternal {
checkExecuteble
//for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
logger.debug("Config for " + analysisName + ": " + config)
beforeCmd
addJobReportBinding("version", getVersion)
if (threads == 0) threads = config.getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
if (vmem == null) {
if (config.contains("vmem")) vmem = config.getAsString("vmem")
else if (!defaultVmem.isEmpty) vmem = defaultVmem
}
if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
jobName = this.analysisName + ":" + firstOutput.getName
}
protected def cmdLine: String
final def commandLine: String = {
preCmdInternal
val cmd = cmdLine
addJobReportBinding("command", cmd)
cmd
}
protected var versionCommand: String = _
protected val versionRegex: Regex = null
def getVersion : String = {
if (versionCommand == null || versionRegex == null) return "N/A"
val buffer = new StringBuffer()
val process = Process(versionCommand).run(ProcessLogger(buffer append _))
if (process.exitValue != 0) {
logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found")
return "N/A"
}
val lines = versionCommand lines_! ProcessLogger(buffer append _)
for (line <- lines) {
line match {
case versionRegex(m) => return m
case _ =>
}
}
logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
return "N/A"
}
}
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala 0 → 100644
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function
import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.collection.JavaConversions._
trait PythonCommandLineFunction extends BiopetCommandLineFunction {
executeble = config.getAsString("python_exe", "python")
@Input(doc="Python script", required=false)
var python_script: File = _
protected var python_script_name : String = _
def setPythonScript(script:String) { setPythonScript(script,"") }
def setPythonScript(script:String, subpackage:String) {
python_script_name = script
python_script = new File(".queue/tmp/" + subpackage + python_script_name)
if (!python_script.getParentFile.exists) python_script.getParentFile.mkdirs
val is = getClass.getResourceAsStream(subpackage + python_script_name)
val os = new FileOutputStream(python_script)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
}
def getPythonCommand() : String = {
required(executeble) + required(python_script)
}
}
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class Sha1sum(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "sha1sum"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
class Sha1sum(val globalConfig: Config) extends BiopetCommandLineFunction {
@Input(doc="Zipped file")
var input: File = _
@Input(doc="Zipped file") var in: File = _
@Output(doc="Unzipped file") var out: File = _
@Output(doc="Unzipped file")
var output: File = _
def commandLine = "sha1sum %s > %s".format(in, out)
executeble = config.getAsString("exe","sha1sum")
def cmdLine = required(executeble) + required(input) + " > " + required(output)
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
//import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class Zcat(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "zcat"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
class Zcat(val globalConfig: Config) extends BiopetCommandLineFunction {
@Input(doc="Zipped file")
var input: File = _
@Input(doc="Zipped file") var in: File = _
@Output(doc="Unzipped file") var out: File = _
@Output(doc="Unzipped file")
var output: File = _
def commandLine = "zcat %s > %s".format(in, out)
executeble = config.getAsString("exe", "zcat")
def cmdLine = required(executeble) + required(input) + " > " + required(output)
}
\ No newline at end of file
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.io.Source._
import scala.sys.process._
class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
analysisName = "cutadapt"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
class Cutadapt(val globalConfig: Config) extends BiopetCommandLineFunction {
@Input(doc="Input fastq file")
var fastq_input: File = _
@Input(doc="Cutadapt exe", required=false)
var cutadapt_exe: File = new File(config.getAsString("exe","/usr/local/bin/cutadapt"))
@Input(doc="Input fastq file") var fastq_input: File = _
@Input(doc="Fastq contams file", required=false) var contams_file: File = _
@Output(doc="Output fastq file") var fastq_output: File = _
@Input(doc="Fastq contams file", required=false)
var contams_file: File = _
@Output(doc="Output fastq file")
var fastq_output: File = _
executeble = config.getAsString("exe","cutadapt")
var default_clip_mode = config.getAsString("default_clip_mode", "3")
var opt_adapter: Set[String] = config.getAsListOfStrings("adapter", Nil).to[Set]
......@@ -28,15 +27,20 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
var opt_minimum_length: String = config.getAsInt("minimum_length", 1).toString
var opt_maximum_length: String = config.getAsString("maximum_length", null)
def init() {
this.addJobReportBinding("version", getVersion)
override val versionRegex = """(.*)""".r
override def afterGraph() {
versionCommand = executeble + " --version"
}
override def beforeCmd() {
this.getContamsFromFile
}
def commandLine = {
init()
def cmdLine = {
if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
required(cutadapt_exe) +
analysisName = getClass.getName
required(executeble) +
// options
repeat("-a", opt_adapter) +
repeat("-b", opt_anywhere) +
......@@ -48,6 +52,7 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
required(fastq_input) +
" > " + required(fastq_output)
} else {
analysisName = getClass.getName + "-ln"
"ln -sf " +
required(fastq_input) +
required(fastq_output)
......@@ -71,24 +76,4 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
} else logger.warn("File : " + contams_file + " does not exist")
}
}
private var version: String = _
var versionCommand = cutadapt_exe + " --version"
var versionRegex = """(.*)"""
def getVersion: String = getVersion(versionCommand, versionRegex)
def getVersion(cmd:String, regex:String) : String = {
val REG = regex.r
if (cmd.! != 0) {
logger.warn("Version command: '" + cmd + "' give a none-zero exit code, version not found")
return "NA"
}
for (line <- cmd.!!.split("\n")) {
line match {
case REG(m) => return m
case _ =>
}
}
logger.warn("Version command: '" + cmd + "' give a exit code 0 but no version was found, executeble oke?")
return "NA"
}
}
\ No newline at end of file
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Fastqc(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "fastqc"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="fastqc executeble", shortName="Fastqc_Exe")
var fastqc_exe: File = new File(config.getAsString("exe","/usr/local/FastQC/FastQC_v0.10.1/fastqc"))
@Argument(doc="java vm executeble", shortName="Java_Exe", required=false)
var java_exe: String = globalConfig.getAsConfig("java").getAsString("exe", "java")
@Argument(doc="kmers", required=false) var kmers: Int = config.getAsInt("kmers", 5)
@Argument(doc="threads", required=false) var threads: Int = config.getAsInt("threads", 4)
@Argument(doc="quiet", required=false) var quiet: Boolean = config.getAsBoolean("quiet", false)
@Argument(doc="noextract", required=false) var noextract: Boolean = config.getAsBoolean("noextract", false)
@Argument(doc="nogroup", required=false) var nogroup: Boolean = config.getAsBoolean("nogroup", false)
class Fastqc(val globalConfig: Config) extends BiopetCommandLineFunction {
@Input(doc="Contaminants", required=false)
var contaminants: File = new File(config.getAsString("contaminants",fastqc_exe.getParent() + "/Contaminants/contaminant_list.txt"))
@Input(doc="Fastq file", shortName="FQ") var fastqfile: File = _
@Output(doc="Output", shortName="out") var output: File = _
var contaminants: File = _
@Input(doc="Fastq file", shortName="FQ")
var fastqfile: File = _
if (config.contains("vmem")) jobResourceRequests :+= "h_vmem=" + config.getAsString("vmem")
@Output(doc="Output", shortName="out")
var output: File = _
executeble = config.getAsString("exe","fastqc")
var java_exe: String = config.getAsConfig("java").getAsString("exe", "java")
var kmers: Int = config.getAsInt("kmers", 5)
var quiet: Boolean = config.getAsBoolean("quiet", false)
var noextract: Boolean = config.getAsBoolean("noextract", false)
var nogroup: Boolean = config.getAsBoolean("nogroup", false)
def init() {
this.addJobReportBinding("version", getVersion)
var maxThreads: Int = config.getAsInt("maxthreads", 24)
if (threads > maxThreads) threads = maxThreads
nCoresRequest = Option(threads)
this.jobNativeArgs :+= "-l h_vmem="+config.getAsString("vmem", "4G")
}
override val versionRegex = """FastQC (.*)""".r
override val defaultThreads = 4
def commandLine = {
init()
required(fastqc_exe) +
override def afterGraph {
this.checkExecuteble
val fastqcDir = executeble.substring(0, executeble.lastIndexOf("/"))
if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
versionCommand = executeble + " --version"
}
def cmdLine = {
required(executeble) +
optional("--java", java_exe) +
optional("--threads",threads) +
optional("--contaminants",contaminants) +
......@@ -50,24 +45,4 @@ class Fastqc(val globalConfig: Config) extends CommandLineFunction {
required(fastqfile) +
required(" > ", output, escape=false)
}
private var version: String = _
var versionCommand = fastqc_exe + " --version"
var versionRegex = """FastQC (.*)"""
def getVersion: String = getVersion(versionCommand, versionRegex)
def getVersion(cmd:String, regex:String) : String = {
val REG = regex.r
if (cmd.! != 0) {
logger.warn("Version command: '" + cmd + "' give a none-zero exit code, version not found")
return "NA"
}
for (line <- cmd.!!.split("\n")) {
line match {
case REG(m) => return m
case _ =>
}
}
logger.warn("Version command: '" + cmd + "' give a exit code 0 but no version was found, executeble oke?")
return "NA"
}
}
\ No newline at end of file
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.io.Source._
import scala.sys.process._
class Sickle(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "sickle"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
class Sickle(val globalConfig: Config) extends BiopetCommandLineFunction {
@Input(doc="R1 input")
var input_R1: File = null
@Input(doc="Sickle exe", required=false) var sickle_exe: File = new File(config.getAsString("exe", "/usr/local/bin/sickle"))
@Input(doc="R1 input") var input_R1: File = null
@Input(doc="R2 input", required=false) var input_R2: File = null
@Output(doc="R1 output") var output_R1: File = null
@Output(doc="R2 output", required=false) var output_R2: File = null
@Output(doc="singles output", required=false) var output_singles: File = null
@Output(doc="stats output") var output_stats: File = null
@Input(doc="qualityType file", required=false) var qualityTypeFile: File = null
@Argument(doc="Quality Type", required=false) var qualityType: String = config.getAsString("qualitytype", null)
@Input(doc="deps", required=false) var deps: List[File] = Nil
@Input(doc="R2 input", required=false)
var input_R2: File = null
var defaultQualityType: String = config.getAsString("defaultqualitytype", "sanger")
@Input(doc="qualityType file", required=false)
var qualityTypeFile: File = _
def init() {
this.addJobReportBinding("version", getVersion)
this.getQualityTypeFromFile
@Output(doc="R1 output")
var output_R1: File = null
@Output(doc="R2 output", required=false)
var output_R2: File = null
@Output(doc="singles output", required=false)
var output_singles: File = null
@Output(doc="stats output")
var output_stats: File = null
executeble = config.getAsString("exe", "sickle")
var qualityType: String = config.getAsString("qualitytype", null)
var defaultQualityType: String = _
override val versionRegex = """sickle version (.*)""".r
override def afterGraph {
if (defaultQualityType == null) defaultQualityType = config.getAsString("defaultqualitytype", "sanger")
if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
versionCommand = executeble + " --version"
}
def commandLine = {
init()
var cmd: String = required(sickle_exe)
override def beforeCmd {
qualityType = getQualityTypeFromFile
}
def cmdLine = {
var cmd: String = required(executeble)
if (input_R2 != null) {
cmd += required("pe") +
required("-r", input_R2) +
......@@ -49,34 +61,15 @@ class Sickle(val globalConfig: Config) extends CommandLineFunction {
" > " + required(output_stats)
}
def getQualityTypeFromFile {
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"))
qualityType = s
return s
}
} else logger.warn("File : " + qualityTypeFile + " does not exist")
}
}
private var version: String = _
var versionCommand = sickle_exe + " --version"
var versionRegex = """sickle version (.*)"""
def getVersion: String = getVersion(versionCommand, versionRegex)
def getVersion(cmd:String, regex:String) : String = {
val REG = regex.r
if (cmd.! != 0) {
logger.warn("Version command: '" + cmd + "' give a none-zero exit code, version not found")
return "NA"
}
for (line <- cmd.!!.split("\n")) {
line match {
case REG(m) => return m
case _ =>
}
}
logger.warn("Version command: '" + cmd + "' give a exit code 0 but no version was found, executeble oke?")
return "NA"
return null
}
}
\ No newline at end of file
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
View file @ bd8a2a63
......@@ -2,19 +2,13 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
//import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class FastqSync(val globalConfig: Config) extends Python {
def this() = this(new Config(Map()))
analysisName = "fastqsync"
val config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
setPythonScript("sync_paired_end_reads.py", "scripts/")
class FastqSync(val globalConfig: Config) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("sync_paired_end_reads.py")
@Input(doc="Start fastq") var input_start_fastq: File = _
@Input(doc="R1 input") var input_R1: File = _
......@@ -23,7 +17,7 @@ class FastqSync(val globalConfig: Config) extends Python {
@Output(doc="R2 output") var output_R2: File = _
var output_stats: File = _
def commandLine = {
def cmdLine = {
getPythonCommand +
required(input_start_fastq) +
required(input_R1) +
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
View file @ bd8a2a63
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.function.Python
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class FastqcToContams(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "getcontams"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
setPythonScript("fastqc_contam.py", "scripts/")
class FastqcToContams(val globalConfig: Config) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("fastqc_contam.py")
@Input(doc="Fastqc output", shortName="fastqc", required=