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
index 8434495c76d81c8fa1e6df2ffcdc612c0f9add17..c57ce72d140cafab19d305730310372cdf001fe1 100644
--- 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
@@ -19,13 +19,15 @@
package nl.lumc.sasc.biopet.pipelines.yamsvp
+import java.io.File
+
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
-import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge, SambambaMarkdup }
-import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
+import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMerge, SambambaMarkdup }
+//import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -35,163 +37,112 @@ import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._
import org.broadinstitute.gatk.queue.engine.JobRunInfo
-class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
+class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
+ qscript =>
def this() = this(null)
var reference: File = config("reference", required = true)
- var finalBamFiles: List[File] = Nil
- /*
- class LibraryOutput extends AbstractLibraryOutput {
- var mappedBamFile: File = _
- }
- class SampleOutput extends AbstractSampleOutput {
- var vcf: Map[String, List[File]] = Map()
- var mappedBamFile: File = _
- }
-*/
- override def init() {
- if (outputDir == null)
- throw new IllegalStateException("Output directory is not specified in the config / argument")
- else if (!outputDir.endsWith("/"))
- outputDir += "/"
- }
+ def makeSample(id: String) = new Sample(id)
+ class Sample(sampleId: String) extends AbstractSample(sampleId) {
- def biopetScript() {
- // write the pipeline here
- // start with QC, alignment, call sambamba, call sv callers, reporting
+ val alignmentDir: String = sampleDir + "alignment/"
+ val svcallingDir: String = sampleDir + "svcalls/"
- // read config and set all parameters for the pipeline
- logger.info("Starting YAM SV Pipeline")
- //runSamplesJobs
- //
+ def makeLibrary(id: String) = new Library(id)
+ class Library(libraryId: String) extends AbstractLibrary(libraryId) {
- }
+ // val runDir: String = alignmentDir + "run_" + libraryId + "/"
- override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
- logger.info("YAM SV Pipeline has run .......................")
- }
- /*
- def runSingleSampleJobs(sampleID: String): SampleOutput = {
- val sampleOutput = new SampleOutput
- var libraryBamfiles: List[File] = List()
- var outputFiles: Map[String, List[File]] = Map()
- var libraryFastqFiles: List[File] = List()
- val sampleDir: String = outputDir + sampleID + "/"
- val alignmentDir: String = sampleDir + "alignment/"
+ val mapping = new Mapping(qscript)
+ mapping.libraryId = libraryId
+ mapping.sampleId = sampleId
- val svcallingDir: String = sampleDir + "svcalls/"
+ protected def addJobs(): Unit = {
+ mapping.input_R1 = config("R1", required = true)
+ mapping.input_R2 = config("R2", required = true)
+ mapping.outputDir = libDir
- sampleOutput.libraries = runLibraryJobs(sampleID)
- for ((libraryID, libraryOutput) <- sampleOutput.libraries) {
- // this is extending the libraryBamfiles list like '~=' in D or .append in Python or .push_back in C++
- libraryBamfiles ++= List(libraryOutput.mappedBamFile)
+ mapping.init
+ mapping.biopetScript
+ qscript.addAll(mapping.functions)
+ }
}
-
- val bamFile: File =
- if (libraryBamfiles.size == 1) {
- // When the sample has only 1 run, make a link in the main alignment directory
- val alignmentlink = Ln(this, libraryBamfiles.head,
- alignmentDir + sampleID + ".merged.bam", true)
- add(alignmentlink, isIntermediate=true)
+ protected def addJobs(): Unit = {
+ addLibsJobs()
+ 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", true)
+ alignmentlink.isIntermediate = true
+ add(alignmentlink)
alignmentlink.out
} else if (libraryBamfiles.size > 1) {
- val mergeSamFiles = new SambambaMerge(this)
+ val mergeSamFiles = new SambambaMerge(qscript)
mergeSamFiles.input = libraryBamfiles
- mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
- add(mergeSamFiles, isIntermediate=true)
+ mergeSamFiles.output = sampleDir + sampleId + ".merged.bam"
+ mergeSamFiles.isIntermediate = true
+ add(mergeSamFiles)
mergeSamFiles.output
} else null
- val bamMarkDup = SambambaMarkdup(this, bamFile)
- add(bamMarkDup)
+ val bamMarkDup = SambambaMarkdup(qscript, bamFile)
+ add(bamMarkDup)
- addAll(BamMetrics(this, bamMarkDup.output, alignmentDir + "metrics/").functions)
+ addAll(BamMetrics(qscript, bamMarkDup.output, alignmentDir + "metrics" + File.separator).functions)
- // create an IGV TDF file
- val tdfCount = IGVToolsCount(this, bamMarkDup.output, config("genomename", default = "hg19"))
- add(tdfCount)
+ // 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"
+ /// 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(this, bamMarkDup.output, this.reference, svcallingDir, cleverDir)
- sampleOutput.vcf += ("clever" -> List(clever.outputvcf))
- add(clever)
+ val cleverDir = svcallingDir + sampleId + ".clever/"
+ val clever = CleverCaller(qscript, bamMarkDup.output, qscript.reference, svcallingDir, cleverDir)
+ add(clever)
- val clever_vcf = Ln(this, clever.outputvcf, svcallingDir + sampleID + ".clever.vcf", relative = true)
- add(clever_vcf)
+ val clever_vcf = Ln(qscript, clever.outputvcf, svcallingDir + sampleId + ".clever.vcf", relative = true)
+ add(clever_vcf)
- val breakdancerDir = svcallingDir + sampleID + ".breakdancer/"
- val breakdancer = Breakdancer(this, bamMarkDup.output, this.reference, breakdancerDir)
- sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputvcf))
- addAll(breakdancer.functions)
+ val breakdancerDir = svcallingDir + sampleId + ".breakdancer/"
+ val breakdancer = Breakdancer(qscript, bamMarkDup.output, qscript.reference, breakdancerDir)
+ addAll(breakdancer.functions)
- val bd_vcf = Ln(this, breakdancer.outputvcf, svcallingDir + sampleID + ".breakdancer.vcf", relative = true)
- add(bd_vcf)
+ val bd_vcf = Ln(qscript, breakdancer.outputvcf, svcallingDir + sampleId + ".breakdancer.vcf", relative = true)
+ add(bd_vcf)
- val dellyDir = svcallingDir + sampleID + ".delly/"
- val delly = Delly(this, bamMarkDup.output, dellyDir)
- sampleOutput.vcf += ("delly" -> List(delly.outputvcf))
- addAll(delly.functions)
+ 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)
+ //
+ }
+ }
- val delly_vcf = Ln(this, delly.outputvcf, svcallingDir + sampleID + ".delly.vcf", relative = true)
- add(delly_vcf)
+ def init() {
+ }
- // for pindel we should use per library config collected into one config file
- // val pindelDir = svcallingDir + sampleID + ".pindel/"
- // val pindel = Pindel(this, analysisBam, this.reference, pindelDir)
- // sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
- // addAll(pindel.functions)
- //
- // val pindel_vcf = Ln(this, pindel.outputvcf, svcallingDir + sampleID + ".pindel.vcf", relative = true)
- // add(pindel_vcf)
- //
- return sampleOutput
+ def biopetScript() {
+ logger.info("Starting YAM SV Pipeline")
+ addSamplesJobs
}
- // Called for each run from a sample
-
- def runSingleLibraryJobs(libraryId: String, sampleID: String): LibraryOutput = {
- val libraryOutput = new LibraryOutput
-
- val alignmentDir: String = outputDir + sampleID + "/alignment/"
- val runDir: String = alignmentDir + "run_" + libraryId + "/"
-
- if (config.contains("R1")) {
- val mapping = new Mapping(this)
-
- // TODO: check and test config[aligner] in json
- // yamsvp/aligner -> value
- // this setting causes error if not defined?
- mapping.aligner = config("aligner", default = "bwa")
- mapping.skipFlexiprep = false
- mapping.skipMarkduplicates = true // we do the dedup marking using Sambamba
-
- mapping.input_R1 = config("R1")
- mapping.input_R2 = config("R2")
- mapping.paired = (mapping.input_R2 != null)
- mapping.RGLB = libraryId
- mapping.RGSM = sampleID
- mapping.RGPL = config("PL")
- mapping.RGPU = config("PU")
- mapping.RGCN = config("CN")
- mapping.outputDir = runDir
-
- mapping.init
- mapping.biopetScript
- addAll(mapping.functions)
-
- // start sambamba dedup
-
- libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
- } else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + libraryId)
- return libraryOutput
- // logger.debug(outputFiles)
- // return outputFiles
+ 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