From 95d45227745ff522c44eb6e90986daf8e2033005 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 24 Sep 2015 16:07:49 +0200
Subject: [PATCH] Move breaking classes
---
.../biopet/extensions/pindel/Pindel.scala | 86 ----------
.../extensions/pindel/PindelCaller.scala | 72 --------
.../extensions/pindel/PindelConfig.scala | 86 ----------
.../sasc/biopet/pipelines/yamsvp/Yamsvp.scala | 155 ------------------
.../src/test/resources/log4j.properties | 25 ---
5 files changed, 424 deletions(-)
delete mode 100644 public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
delete mode 100644 public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
delete mode 100644 public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
delete mode 100644 public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
delete mode 100644 public/yamsvp/src/test/resources/log4j.properties
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
deleted file mode 100644
index 107955334..000000000
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+++ /dev/null
@@ -1,86 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.extensions.pindel
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-/// Pindel is actually a mini pipeline executing binaries from the pindel package
-class Pindel(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "Input file (bam)")
- var input: File = _
-
- @Input(doc = "Reference Fasta file")
- var reference: File = _
-
- @Argument(doc = "Work directory")
- var workdir: String = _
-
- // @Output(doc = "Pindel VCF output")
- // lazy val outputvcf: File = {
- // new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
- // }
-
- @Output(doc = "Pindel config")
- lazy val configfile: File = {
- new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
- }
- @Output(doc = "Pindel raw output")
- lazy val outputvcf: File = {
- new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
- }
-
- override def init() {
- }
-
- def biopetScript() {
- // read config and set all parameters for the pipeline
- logger.info("Starting Pindel configuration")
-
- val cfg = PindelConfig(this, input, this.configfile)
- outputFiles += ("pindel_cfg" -> cfg.output)
- add(cfg)
-
- val output: File = this.outputvcf
- val pindel = PindelCaller(this, cfg.output, output)
- add(pindel)
- outputFiles += ("pindel_tsv" -> pindel.output)
-
- // val output_vcf: File = this.outputvcf
- // convert this tsv to vcf using the python script
-
- }
-
- // private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.tsv"
-}
-
-object Pindel extends PipelineCommand {
- def apply(root: Configurable, input: File, reference: File, runDir: String): Pindel = {
- val pindel = new Pindel(root)
- pindel.input = input
- pindel.reference = reference
- pindel.workdir = runDir
- // run the following for activating the pipeline steps
- pindel.init()
- pindel.biopetScript()
- pindel
- }
-}
\ No newline at end of file
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
deleted file mode 100644
index cbe957e79..000000000
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ /dev/null
@@ -1,72 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.extensions.pindel
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
-
-class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
- executable = config("exe", default = "pindel", freeVar = false)
-
- override def defaultCoreMemory = 5.0
- override def defaultThreads = 8
-
- override def versionRegex = """Pindel version:? (.*)""".r
- override def versionExitcode = List(1)
- override def versionCommand = executable
-
- @Input(doc = "The pindel configuration file")
- var input: File = _
-
- @Input(doc = "Fasta reference")
- var reference: File = config("reference")
-
- // this is a pointer to where the results files will be stored
- // inside this directory, we can expect files named:
- // <prefix>_D
- // <prefix>_SI
- // <prefix>_I
- // <prefix>_TR
- @Argument(doc = "Work directory")
- var workdir: String = _
-
- @Output(doc = "Pindel VCF output")
- var output: File = _
-
- var window_size: Option[Int] = config("window_size", default = 5)
-
- override def beforeCmd() {
- }
-
- def cmdLine = required(executable) +
- "-i " + required(input) +
- "-f " + required(reference) +
- "-o " + required(output) +
- optional("-w", window_size) +
- optional("-T", nCoresRequest)
-}
-
-object PindelCaller {
- def apply(root: Configurable, input: File, output: File): PindelCaller = {
- val caller = new PindelCaller(root)
- caller.input = input
- caller.output = output
- caller
- }
-}
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
deleted file mode 100644
index 55127e59f..000000000
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+++ /dev/null
@@ -1,86 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.extensions.pindel
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
-
-class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction {
- javaMainClass = getClass.getName
- @Input(doc = "Bam File")
- var input: File = _
-
- @Output(doc = "Output Config file")
- var output: File = _
-
- @Argument(doc = "Insertsize")
- var insertsize: Option[Int] = _
-
- override def commandLine = super.commandLine +
- "-i" + required(input) +
- "-s" + required(insertsize) +
- "-o" + required(output)
-}
-
-object PindelConfig extends ToolCommand {
- def apply(root: Configurable, input: File, output: File): PindelConfig = {
- val conf = new PindelConfig(root)
- conf.input = input
- conf.output = output
- conf
- }
-
- def apply(root: Configurable, input: File, outputDir: String): PindelConfig = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): PindelConfig = {
- apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.cfg"
-
- case class Args(inputbam: File = null, samplelabel: Option[String] = None, insertsize: Option[Int] = None) extends AbstractArgs
-
- class OptParser extends AbstractOptParser {
- opt[File]('i', "inputbam") required () valueName "<bamfile/path>" action { (x, c) =>
- c.copy(inputbam = x)
- } text "Please specify the input bam file"
- opt[String]('l', "samplelabel") valueName "<sample label>" action { (x, c) =>
- c.copy(samplelabel = Some(x))
- } text "Sample label is missing"
- opt[Int]('s', "insertsize") valueName "<insertsize>" action { (x, c) =>
- c.copy(insertsize = Some(x))
- } text "Insertsize is missing"
- }
-
- /**
- * @param args the command line arguments
- */
- def main(args: Array[String]): Unit = {
- val argsParser = new OptParser
- val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
-
- val input: File = commandArgs.inputbam
-
- }
-}
-
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
deleted file mode 100644
index a0ade5706..000000000
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ /dev/null
@@ -1,155 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-/*
- * Structural variation calling
- */
-
-package nl.lumc.sasc.biopet.pipelines.yamsvp
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.extensions.Ln
-import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
-import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
-import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMarkdup, SambambaMerge }
-//import nl.lumc.sasc.biopet.extensions.pindel.Pindel
-import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
-import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.engine.JobRunInfo
-import org.broadinstitute.gatk.queue.function._
-
-class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
- qscript =>
- def this() = this(null)
- def summaryFile = null
- def summaryFiles = Map()
- def summarySettings = Map()
-
- var reference: File = config("reference")
-
- def makeSample(id: String) = new Sample(id)
- class Sample(sampleId: String) extends AbstractSample(sampleId) {
-
- def summaryFiles = Map()
- def summaryStats = Map()
-
- val alignmentDir: String = sampleDir + "alignment/"
- val svcallingDir: String = sampleDir + "svcalls/"
-
- def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
- // val runDir: String = alignmentDir + "run_" + libraryId + "/"
- def summaryFiles = Map()
- def summaryStats = Map()
-
- val mapping = new Mapping(qscript)
- mapping.libId = Some(libraryId)
- mapping.sampleId = Some(sampleId)
-
- protected def addJobs(): Unit = {
- mapping.input_R1 = config("R1")
- mapping.input_R2 = config("R2")
- mapping.outputDir = libDir
-
- mapping.init()
- mapping.biopetScript()
- qscript.addAll(mapping.functions)
- }
- }
- protected def addJobs(): Unit = {
- val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
-
- val bamFile: File = if (libraryBamfiles.size == 1) {
- val alignmentlink = Ln(qscript, libraryBamfiles.head,
- alignmentDir + sampleId + ".merged.bam", relative = true)
- alignmentlink.isIntermediate = true
- add(alignmentlink)
- alignmentlink.output
- } else if (libraryBamfiles.size > 1) {
- val mergeSamFiles = new SambambaMerge(qscript)
- mergeSamFiles.input = libraryBamfiles
- mergeSamFiles.output = sampleDir + sampleId + ".merged.bam"
- mergeSamFiles.isIntermediate = true
- add(mergeSamFiles)
- mergeSamFiles.output
- } else null
-
- val bamMarkDup = SambambaMarkdup(qscript, bamFile)
- add(bamMarkDup)
-
- addAll(BamMetrics(qscript, bamMarkDup.output, alignmentDir + "metrics" + File.separator).functions)
-
- // create an IGV TDF file
- val tdfCount = IGVToolsCount(qscript, bamMarkDup.output, config("genome_name", default = "hg19"))
- add(tdfCount)
-
- /// bamfile will be used as input for the SV callers. First run Clever
- // val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
-
- val cleverDir = svcallingDir + sampleId + ".clever/"
- val clever = CleverCaller(qscript, bamMarkDup.output, qscript.reference, svcallingDir, cleverDir)
- add(clever)
-
- val clever_vcf = Ln(qscript, clever.outputvcf, svcallingDir + sampleId + ".clever.vcf", relative = true)
- add(clever_vcf)
-
- val breakdancerDir = svcallingDir + sampleId + ".breakdancer/"
- val breakdancer = Breakdancer(qscript, bamMarkDup.output, qscript.reference, breakdancerDir)
- addAll(breakdancer.functions)
-
- val bd_vcf = Ln(qscript, breakdancer.outputvcf, svcallingDir + sampleId + ".breakdancer.vcf", relative = true)
- add(bd_vcf)
-
- val dellyDir = svcallingDir + sampleId + ".delly/"
- val delly = Delly(qscript, bamMarkDup.output, dellyDir)
- addAll(delly.functions)
-
- val delly_vcf = Ln(qscript, delly.outputvcf, svcallingDir + sampleId + ".delly.vcf", relative = true)
- add(delly_vcf)
-
- // for pindel we should use per library config collected into one config file
- // val pindelDir = svcallingDir + sampleID + ".pindel/"
- // val pindel = Pindel(qscript, analysisBam, this.reference, pindelDir)
- // sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
- // addAll(pindel.functions)
- //
- // val pindel_vcf = Ln(qscript, pindel.outputvcf, svcallingDir + sampleID + ".pindel.vcf", relative = true)
- // add(pindel_vcf)
- //
- }
- }
-
- def addMultiSampleJobs() = {}
-
- def init() {
- }
-
- def biopetScript() {
- logger.info("Starting YAM SV Pipeline")
- addSamplesJobs()
- }
-
- override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
- logger.info("YAM SV Pipeline has run .......................")
- }
-}
-
-object Yamsvp extends PipelineCommand
\ No newline at end of file
diff --git a/public/yamsvp/src/test/resources/log4j.properties b/public/yamsvp/src/test/resources/log4j.properties
deleted file mode 100644
index 501af6758..000000000
--- a/public/yamsvp/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,25 +0,0 @@
-#
-# Biopet is built on top of GATK Queue for building bioinformatic
-# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-# should also be able to execute Biopet tools and pipelines.
-#
-# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-#
-# Contact us at: sasc@lumc.nl
-#
-# A dual licensing mode is applied. The source code within this project that are
-# not part of GATK Queue is freely available for non-commercial use under an AGPL
-# license; For commercial users or users who do not want to follow the AGPL
-# license, please contact us to obtain a separate license.
-#
-
-# Set root logger level to DEBUG and its only appender to A1.
-log4j.rootLogger=ERROR, A1
-
-# A1 is set to be a ConsoleAppender.
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
-
-# A1 uses PatternLayout.
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
--
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