From 5a4df7151678303548bfb3b0d063ba51ab3edbb6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Jun 2014 11:36:59 +0200
Subject: [PATCH] Added merge config
---
.../src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala | 9 ++++++---
.../main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala | 2 +-
.../main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala | 2 +-
.../biopet/pipelines/flexiprep/scripts/FastqSync.scala | 2 +-
.../pipelines/flexiprep/scripts/FastqcToContams.scala | 2 +-
.../pipelines/flexiprep/scripts/FastqcToQualtype.scala | 2 +-
.../biopet/pipelines/flexiprep/scripts/Seqstat.scala | 2 +-
.../biopet/pipelines/flexiprep/scripts/Summarize.scala | 2 +-
.../nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala | 2 +-
.../java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala | 2 +-
.../java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala | 2 +-
.../java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala | 2 +-
.../nl/lumc/sasc/biopet/wrappers/aligners/Star.scala | 4 ++--
13 files changed, 19 insertions(+), 16 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
index f09971730..2764aebf0 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
@@ -5,17 +5,20 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
//import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.commandline._
import java.io.File
+import scala.sys.process._
class Ln(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "ln"
- val config: Config = globalConfig.getAsConfig(this.analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Input file") var in: File = _
@Output(doc="Link destination") var out: File = _
-
- def commandLine = "ln -sf %s %s".format(in, out)
+
+ def commandLine = {
+ "ln -sf " + required(in) + required(out)
+ }
}
object Ln {
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
index d89e3d9ef..2dded92c2 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
@@ -8,7 +8,7 @@ import java.io.File
class Sha1sum(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "sha1sum"
- val config: Config = globalConfig.getAsConfig("sha1sum")
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Zipped file") var in: File = _
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 de8b4efdc..206d4bd0d 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
@@ -8,7 +8,7 @@ import java.io.File
class Zcat(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "zcat"
- val config: Config = globalConfig.getAsConfig("zcat")
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Zipped file") var in: File = _
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
index 131327f65..4b5f179c7 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
@@ -10,7 +10,7 @@ import java.io.File
class FastqSync(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "fastqsync"
- val config: Config = globalConfig.getAsConfig(analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
index f72c91277..a0c4e9ff2 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
@@ -9,7 +9,7 @@ import java.io.File
class FastqcToContams(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "getcontams"
- val config: Config = globalConfig.getAsConfig(analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
index bbdaefa1f..346d88d90 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
@@ -9,7 +9,7 @@ import java.io.File
class FastqcToQualtype(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "getqualtype"
- val config: Config = globalConfig.getAsConfig(analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
index 003b07535..b046872d2 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -9,7 +9,7 @@ import java.io.File
class Seqstat(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "seqstat"
- val config: Config = globalConfig.getAsConfig(analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
index fec2feccc..2375ffaff 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
@@ -9,7 +9,7 @@ import java.io.File
class Summarize(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "flexiprep_sumarize"
- val config: Config = globalConfig.getAsConfig(analysisName)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
index b9bfbaff2..c4c407ec3 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
@@ -10,7 +10,7 @@ import scala.sys.process._
class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
analysisName = "cutadapt"
- val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("cutadapt"), globalConfig)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Cutadapt exe", required=false)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
index 333581a52..36e2e16d7 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
@@ -9,7 +9,7 @@ import scala.sys.process._
class Fastqc(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "fastqc"
- val config: Config = globalConfig.getAsConfig("fastqc")
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="fastqc executeble", shortName="Fastqc_Exe")
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
index bb9b3ac56..156c2cefa 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
@@ -10,7 +10,7 @@ import scala.sys.process._
class Sickle(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "sickle"
- val config: Config = globalConfig.getAsConfig("sickle")
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Sickle exe", required=false) var sickle_exe: File = new File(config.getAsString("exe", "/usr/local/bin/sickle"))
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
index 905b56f32..f6a5e70f1 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
@@ -9,7 +9,7 @@ import scala.sys.process._
class Bwa(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
this.analysisName = "bwa"
- val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("bwa"), globalConfig)
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Argument(doc="Bwa executeble", shortName="bwa_exe", required=false) var bwa_exe: String = config.getAsString("exe", "/usr/local/bin/bwa")
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
index 0cca136cb..663344054 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
@@ -8,8 +8,8 @@ import scala.sys.process._
class Star(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
- this.analysisName = "STAR"
- val config: Config = globalConfig.getAsConfig("star")
+ this.analysisName = "star"
+ val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Argument(doc="STAR executeble", shortName="star_exe", required=false)
--
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