From b808493584a7de36bd63d54e356584720dbc4e98 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Feb 2015 10:42:01 +0100
Subject: [PATCH] Remove required from config calls
---
.../nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala | 4 ++--
.../nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala | 2 +-
.../sasc/biopet/pipelines/gatk/GatkVariantcalling.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala | 6 +++---
.../main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala | 2 +-
.../biopet/extensions/picard/CollectGcBiasMetrics.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala | 3 ---
.../nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala | 7 +------
.../scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala | 2 +-
16 files changed, 18 insertions(+), 26 deletions(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index 147398ac7..3d1b55850 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
- jarFile = config("gatk_jar", required = true)
+ jarFile = config("gatk_jar")
override val defaultVmem = "7G"
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
- reference_sequence = config("reference", required = true)
+ reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
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 c76139133..be4566211 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
@@ -35,7 +35,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var jointGenotyping: Boolean = config("joint_genotyping", default = false)
var singleSampleCalling = config("single_sample_calling", default = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 8bac4aaf6..47715e26a 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var rawVcfInput: File = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "OutputName", required = false)
var outputName: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 1a3f56588..1e94c21be 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -51,7 +51,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
var functions: Seq[QFunction]
final def script() {
- outputDir = config("output_dir", required = true)
+ outputDir = config("output_dir")
if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index e192a845b..9ac74448e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index a7bfeab78..1db8f6d67 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "ref")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Input(doc = "The genome prefix.")
- var genome: File = config("genome", required = true)
+ var genome: File = config("genome")
@Input(doc = "The hash prefix")
- var hash: File = config("hash", required = true)
+ var hash: File = config("hash")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index e0b8bd68b..98ee6de52 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "Bowtie index", shortName = "bti")
- var bowtie_index: File = config("bowtie_index", required = true)
+ var bowtie_index: File = config("bowtie_index")
@Argument(doc = "Output Directory")
var outputDir: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index bfd0a5846..3298702fc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var fastq: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index fc790b183..74cdad0ce 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index b857eea01..255811561 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
var saiR2: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index 51f9a0f30..8bbf91847 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var sai: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 7ffcb50d8..9cab9bfc9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
var outputSummary: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "Window size", required = false)
var windowSize: Option[Int] = config("windowsize")
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 92d0b9f63..b7353b2ad 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -30,9 +30,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
@Test def testApply: Unit = {
ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
- intercept[IllegalStateException] {
- ConfigTest.config("m1", Nil, "notexist")
- }
}
@Test def testMergeConfigs: Unit = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 1b493f2e1..55f672cc1 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC.classB.get("k1").asString shouldBe "c1"
classC.classB.classA.get("k1").asString shouldBe "c1"
- classC.get("notexist") shouldBe null
- intercept[IllegalStateException] {
- classC.get("notexist", required = true)
- }
classC.get("notexist", default = "default").asString shouldBe "default"
classC.get("k1", freeVar = false).asString shouldBe "c1"
@@ -47,11 +43,10 @@ abstract class Cfg extends Configurable {
def get(key: String,
default: String = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null) = {
- config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
+ config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
}
}
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 ed55ca382..77dba4b14 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
@@ -60,7 +60,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
- val inputFastq: File = config("R1", required = true)
+ val inputFastq: File = config("R1")
val prefixFastq: File = createFile(".prefix.fastq")
val flexiprep = new Flexiprep(qscript)
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 206c92a69..6e7257c7d 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
def this() = this(null)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var finalBamFiles: List[File] = Nil
/*
class LibraryOutput extends AbstractLibraryOutput {
--
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