From 2fb73c969a06a5baf18885672952c822100ce3f7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 May 2014 15:44:51 +0200
Subject: [PATCH] - Standerize config
---
.../src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala | 5 ++---
.../main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala | 4 ++--
.../main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala | 4 ++--
.../main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala | 4 ++--
.../src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala | 4 ++--
.../src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala | 7 ++++---
6 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
index 00a908225..51aa345d3 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
@@ -9,10 +9,10 @@ import scala.sys.process._
class Bwa(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "bwa"
- var config: Config = _
+ val config: Config = globalConfig.getAsConfig("bwa")
@Argument(doc="Bwa executeble", shortName="bwa_exe", required=false) var bwa_exe: String = _
- @Input(doc="The reference file for the bam files.", shortName="R", required=false) var referenceFile: File = _
+ @Input(doc="The reference file for the bam files.", shortName="R") var referenceFile: File = _
@Input(doc="Fastq file R1", shortName="R1") var R1: File = _
@Input(doc="Fastq file R2", shortName="R2", required=false) var R2: File = _
@Output(doc="Output file SAM", shortName="output") var output: File = _
@@ -21,7 +21,6 @@ class Bwa(val globalConfig: Config) extends CommandLineFunction {
@Argument(doc="M", shortName="M", required=false) var M: Boolean = false
def init() {
- config = Config.mergeConfigs(globalConfig.getAsConfig("bwa"), globalConfig)
bwa_exe = config.getAsString("exe", "/usr/local/bin/bwa")
M = config.getAsBoolean("M", true)
jobResourceRequests :+= "h_vmem=" + config.getAsString("vmem", "6G")
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
index dbe65357e..644326bef 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
@@ -7,10 +7,10 @@ import java.io.File
import scala.io.Source._
import scala.sys.process._
-class Cutadapt(private var globalConfig: Config) extends CommandLineFunction {
+class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
analysisName = "cutadapt"
- var config: Config = globalConfig.getAsConfig("cutadapt")
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("cutadapt"), globalConfig)
@Input(doc="Cutadapt exe", required=false)
var cutadapt_exe: File = new File(config.getAsString("exe","/usr/local/bin/cutadapt"))
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala
index 55394a44c..f88be9c15 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala
@@ -6,10 +6,10 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
-class Fastqc(private var globalConfig: Config) extends CommandLineFunction {
+class Fastqc(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "fastqc"
- var config: Config = globalConfig.getAsConfig("fastqc")
+ val config: Config = globalConfig.getAsConfig("fastqc")
@Input(doc="fastqc executeble", shortName="Fastqc_Exe")
var fastqc_exe: File = new File(config.getAsString("exe","/usr/local/FastQC/FastQC_v0.10.1/fastqc"))
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala
index facb378da..3c39d8760 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala
@@ -7,10 +7,10 @@ import java.io.File
import scala.io.Source._
import scala.sys.process._
-class Sickle(private var globalConfig: Config) extends CommandLineFunction {
+class Sickle(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "sickle"
- var config: Config = globalConfig.getAsConfig("sickle")
+ val config: Config = globalConfig.getAsConfig("sickle")
@Input(doc="Sickle exe", required=false) var sickle_exe: File = new File("/usr/local/bin/sickle")
@Input(doc="R1 input") var input_R1: File = null
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
index 079488837..c6c241b6b 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
@@ -6,10 +6,10 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
-class Star(private var globalConfig: Config) extends CommandLineFunction {
+class Star(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "STAR"
- var config: Config = Config.mergeConfigs(globalConfig.getAsConfig("star"), globalConfig)
+ val config: Config = globalConfig.getAsConfig("star")
@Argument(doc="STAR executeble", shortName="star_exe", required=false)
var star_exe: String = config.getAsString("exe", "/usr/local/bin/STAR")
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
index 36e31cfbc..f307616d3 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
@@ -5,9 +5,10 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
-class Zcat(private var config: Config) extends CommandLineFunction {
- def this() = this(new Config(Map()))
- this.analysisName = "zcat"
+class Zcat(val globalConfig: Config) extends CommandLineFunction {
+ def this() = this(new Config(Map()))
+ this.analysisName = "zcat"
+ val config: Config = globalConfig.getAsConfig("zcat")
@Input(doc="Zipped file") var in: File = _
@Output(doc="Unzipped file") var out: File = _
--
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