From 29f9b30fefccb2398a00d36363acec20a1b8e8d6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 13:25:03 +0100
Subject: [PATCH] Name change
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala | 2 +-
6 files changed, 6 insertions(+), 6 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 6ee6e73f6..c260f4561 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
@@ -56,7 +56,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline.biopetScript
addAll(gatkPipeline.functions)
- addPerSampleJobs()
+ addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
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 c9b18c1be..88600e576 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
@@ -151,7 +151,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
def biopetScript(): Unit = {
- addPerSampleJobs
+ addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
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 0857be0ef..0217615d1 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
@@ -128,7 +128,7 @@ trait MultiSampleQScript extends BiopetQScript {
protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
- final def addPerSampleJobs() {
+ final def addSamplesJobs() {
if (onlySamples.isEmpty) {
samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
addMultiSampleJobs()
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 26b070704..b06c01f57 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
@@ -102,7 +102,7 @@ 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")
- addPerSampleJobs
+ addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
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 9bf06c4f0..5360b4ac7 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
@@ -30,7 +30,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
}
def biopetScript() {
- this.addPerSampleJobs()
+ addSamplesJobs()
}
def makeSample(id: String) = new Sample(id)
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 6c65e21bd..03be2ded6 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
@@ -151,7 +151,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
tagsLibrary = cdl.output
}
- addPerSampleJobs
+ addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
--
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