From 21182480323d51e8ecff72b56aa8668cb921dd1a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 27 Feb 2015 16:30:52 +0100
Subject: [PATCH] Make samples and libraries Summarizable
---
.../lumc/sasc/biopet/pipelines/basty/Basty.scala | 15 +++++++++++++++
.../sasc/biopet/pipelines/gatk/GatkPipeline.scala | 8 ++++++++
.../sasc/biopet/core/MultiSampleQScript.scala | 11 ++++++++---
.../pipelines/MultisamplePipelineTemplate.scala | 14 ++++++++++++++
.../nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 8 ++++++++
.../sasc/biopet/pipelines/kopisu/Kopisu.scala | 14 ++++++++++++++
.../nl/lumc/sasc/biopet/pipelines/sage/Sage.scala | 14 ++++++++++++++
7 files changed, 81 insertions(+), 3 deletions(-)
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 506b3433e..4ae4dc3c2 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -31,10 +31,24 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
var gatkPipeline: GatkPipeline = new GatkPipeline(qscript)
+ def summaryFile: File = new File(outputDir, "Sage.summary.json")
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summarySettings: Map[String, Any] = Map()
+
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
protected def addJobs(): Unit = {}
}
@@ -56,6 +70,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def biopetScript() {
gatkPipeline.biopetScript
addAll(gatkPipeline.functions)
+ addSummaryQScript(gatkPipeline)
addSamplesJobs()
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 54370bf2f..c33f8318f 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -49,8 +49,16 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
val mapping = new Mapping(qscript)
mapping.sampleId = Some(sampleId)
mapping.libId = Some(libId)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index c93cfa7a4..c153011bb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -18,13 +18,16 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.core.config.{ Config }
+import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Argument }
/**
* This trait creates a structured way of use multisample pipelines
*/
-trait MultiSampleQScript extends BiopetQScript {
+trait MultiSampleQScript extends SummaryQScript {
+ qscript =>
+
@Argument(doc = "Only Sample", shortName = "sample", required = false)
private val onlySamples: List[String] = Nil
@@ -34,7 +37,7 @@ trait MultiSampleQScript extends BiopetQScript {
* Sample class with basic functions build in
* @param sampleId
*/
- abstract class AbstractSample(val sampleId: String) {
+ abstract class AbstractSample(val sampleId: String) extends Summarizable {
/** Overrules config of qscript with default sample */
val config = new ConfigFunctions(defaultSample = sampleId)
@@ -42,7 +45,7 @@ trait MultiSampleQScript extends BiopetQScript {
* Library class with basic functions build in
* @param libId
*/
- abstract class AbstractLibrary(val libId: String) {
+ abstract class AbstractLibrary(val libId: String) extends Summarizable {
/** Overrules config of qscript with default sample and default library */
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
@@ -51,6 +54,7 @@ trait MultiSampleQScript extends BiopetQScript {
currentSample = Some(sampleId)
currentLib = Some(libId)
addJobs()
+ addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
currentLib = None
currentSample = None
}
@@ -87,6 +91,7 @@ trait MultiSampleQScript extends BiopetQScript {
final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
addJobs()
+ addSummarizable(this, "pipeline", Some(sampleId))
currentSample = None
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
index 7d46c4b8f..b3233ecfe 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
@@ -22,11 +22,25 @@ import org.broadinstitute.gatk.queue.QScript
class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
+ def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summarySettings: Map[String, Any] = Map()
+
def makeSample(id: String) = new Sample(id)
+
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
protected def addJobs(): Unit = {
// Library jobs
}
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 d23fa37b9..dff784223 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
@@ -51,8 +51,16 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
val mapping = new Mapping(qscript)
mapping.libId = Some(libId)
mapping.sampleId = Some(sampleId)
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
index 94b3bcbe6..ee755a384 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
@@ -33,10 +33,24 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
addSamplesJobs()
}
+ def summaryFile: File = new File(outputDir, "Kopisu.summary.json")
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summarySettings: Map[String, Any] = Map()
+
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def addJobs(): Unit = {
}
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index a3a148331..de8cb8f5d 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -58,10 +58,24 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
)
), super.defaults)
+ def summaryFile: File = new File(outputDir, "Sage.summary.json")
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summarySettings: Map[String, Any] = Map()
+
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = Map()
+
val inputFastq: File = config("R1")
val prefixFastq: File = createFile(".prefix.fastq")
--
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