From 7734e7d38d285219579c88bdd4798fdfe6cc1b4d Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 29 Jan 2015 14:33:54 +0100
Subject: [PATCH] Added changes for new sampling handling
---
.../sasc/biopet/pipelines/carp/Carp.scala | 137 ++++++++----------
1 file changed, 61 insertions(+), 76 deletions(-)
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index a69ec4d32..dfef64132 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -15,13 +15,15 @@
*/
package nl.lumc.sasc.biopet.pipelines.carp
+import java.io.File
+
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star, Bowtie, Stampy }
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
@@ -32,14 +34,60 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
* This pipeline performs QC,mapping and peak calling
*/
class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
+ qscript =>
def this() = this(null)
- class LibraryOutput extends AbstractLibraryOutput {
- var mappedBamFile: File = _
- }
+ override def defaults = ConfigUtils.mergeMaps(Map(
+ "mapping" -> Map("skip_markduplicates" -> true)
+ ), super.defaults)
+
+ def makeSample(id: String) = new Sample(id)
+ class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def makeLibrary(id: String) = new Library(id)
+ class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ val mapping = new Mapping(qscript)
+
+ def addJobs(): Unit = {
+ if (config.contains("R1")) {
+ mapping.input_R1 = config("R1")
+ if (config.contains("R2")) mapping.input_R2 = config("R2")
+ mapping.libraryId = libraryId
+ mapping.sampleId = sampleId
+ mapping.outputDir = libDir
+
+ mapping.init
+ mapping.biopetScript
+ addAll(mapping.functions)
+
+ } else logger.error("Sample: " + sampleId + ": No R1 found for library: " + libraryId)
+ }
+ }
+
+ val bamFile = new File(sampleDir + sampleId + ".bam")
+ val controls: List[String] = config("control", default = Nil)
+
+ def addJobs(): Unit = {
+ addLibsJobs()
+ val bamFiles = libraries.map(_._2.mapping.finalBamFile).toList
+ if (bamFiles.length == 1) {
+ add(Ln(qscript, bamFiles.head, bamFile))
+ val oldIndex = new File(bamFiles.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ val newIndex = new File(bamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ add(Ln(qscript, oldIndex, newIndex))
+ } else if (bamFiles.length > 1) {
+ val merge = new MergeSamFiles(qscript)
+ merge.input = bamFiles
+ merge.sortOrder = "coordinate"
+ merge.output = bamFile
+ add(merge)
+ }
- class SampleOutput extends AbstractSampleOutput {
- var mappedBamFile: File = _
+ val macs2 = new Macs2CallPeak(qscript)
+ macs2.treatment = bamFile
+ macs2.name = sampleId
+ macs2.outputdir = sampleDir + "macs2/" + macs2.name + "/"
+ add(macs2)
+ }
}
def init() {
@@ -52,84 +100,21 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
// Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
logger.info("Starting CArP pipeline")
- runSamplesJobs
-
- for (sample <- getSamples) {
- val controls: List[String] = config("control", sample = sample, default = Nil)
+ addSamplesJobs
- for (control <- controls) {
- if (!getSamples.exists(_ == control))
+ for ((sampleId, sample) <- samples) {
+ for (control <- sample.controls) {
+ if (!samples.exists(_ == control))
throw new IllegalStateException("For sample: " + sample + " this control: " + control + " does not exist")
val macs2 = new Macs2CallPeak(this)
- macs2.treatment = samplesOutput(sample).mappedBamFile
- macs2.control = samplesOutput(control).mappedBamFile
+ macs2.treatment = sample.bamFile
+ macs2.control = samples(control).bamFile
macs2.name = sample + "_VS_" + control
- macs2.outputdir = globalSampleDir + sample + "/" + "macs2/" + macs2.name + "/"
+ macs2.outputdir = sample.sampleDir + "/" + "macs2/" + macs2.name + "/"
add(macs2)
}
}
}
-
- def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
- val sampleOutput = new SampleOutput
- val sampleID: String = getCurrentSample
- val sampleDir = globalSampleDir + sampleID + "/"
-
- sampleOutput.libraries = runLibraryJobs(sampleConfig)
- val bamfiles = sampleOutput.libraries.map(_._2.mappedBamFile).toList
- sampleOutput.mappedBamFile = new File(sampleDir + sampleID + ".bam")
- if (bamfiles.length == 1) {
- add(Ln(this, bamfiles.head, sampleOutput.mappedBamFile))
- val oldIndex = new File(bamfiles.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex = new File(sampleOutput.mappedBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
- add(Ln(this, oldIndex, newIndex))
- } else if (bamfiles.length > 1) {
- val merge = new MergeSamFiles(this)
- merge.input = bamfiles
- merge.sortOrder = "coordinate"
- merge.output = sampleOutput.mappedBamFile
- add(merge)
- }
-
- val macs2 = new Macs2CallPeak(this)
- macs2.treatment = sampleOutput.mappedBamFile
- macs2.name = sampleID
- macs2.outputdir = sampleDir + "macs2/" + macs2.name + "/"
- add(macs2)
-
- return sampleOutput
- }
-
- def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
- val libraryOutput = new LibraryOutput
-
- val runID: String = getCurrentLibrary
- val sampleID: String = getCurrentSample
- val runDir: String = globalSampleDir + sampleID + "/run_" + runID + "/"
-
- if (runConfig.contains("R1")) {
- val mapping = new Mapping(this)
-
- mapping.skipMarkduplicates = config("skip_markduplicates", default = true) // we do the dedup marking using Sambamba
-
- mapping.input_R1 = new File(runConfig("R1").toString)
- if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
- mapping.RGLB = runConfig("ID").toString
- mapping.RGSM = sampleConfig("ID").toString
- if (runConfig.contains("PL")) mapping.RGPL = runConfig("PL").toString
- if (runConfig.contains("PU")) mapping.RGPU = runConfig("PU").toString
- if (runConfig.contains("CN")) mapping.RGCN = runConfig("CN").toString
- mapping.outputDir = runDir
-
- mapping.init
- mapping.biopetScript
- addAll(mapping.functions)
-
- libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
- } else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
- return libraryOutput
- }
-
}
object Carp extends PipelineCommand
--
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