From a9f86490477ba92565a691f7e4329efb710da3c3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 11:51:38 +0100
Subject: [PATCH] Switch to new multisample part
---
.../sasc/biopet/pipelines/kopisu/Kopisu.scala | 28 +++++++++----------
1 file changed, 13 insertions(+), 15 deletions(-)
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 3b503759c..9bf06c4f0 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
@@ -25,31 +25,29 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
@Input(doc = "Input bamfile", required = true)
var bamFile: File = config("bam")
- class LibraryOutput extends AbstractLibraryOutput {
- }
-
- class SampleOutput extends AbstractSampleOutput {
- }
-
def init() {
if (!outputDir.endsWith("/")) outputDir += "/"
}
def biopetScript() {
- runSamplesJobs
+ this.addPerSampleJobs()
}
- // Called for each sample
- def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
- val sampleOutput = new SampleOutput
+ 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) {
+ def addJobs(): Unit = {
+
+ }
+ }
+
+ def addJobs(): Unit = {
- return sampleOutput
+ }
}
- // Called for each run from a sample
- def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
- val libraryOutput = new LibraryOutput
- return libraryOutput
+ def addMultiSampleJobs(): Unit = {
}
}
--
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