Commit 7d00bf07 authored by Sander Bollen's avatar Sander Bollen
Browse files

no more failing tests :-)

parent 6e5f1478
......@@ -138,7 +138,7 @@ Setting up the pipeline is done within the pipeline itself, fine-tuning is alway
For our new pipeline, one should setup the (default) config options.
Since our pipeline is called `HelloPipeline`, the root of the configNamespace for our pipeline will be called `hellopipeline` (lowercaps).
Since our pipeline is called `HelloPipeline`, the root of the namespace for our pipeline will be called `hellopipeline` (lowercaps).
```json
{
......
......@@ -34,7 +34,7 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
#### Required configuration values
| configNamespace | Name | Type | Default | Function |
| namespace | Name | Type | Default | Function |
| --------- | ---- | ---- | ------- | -------- |
| shiva | variantcallers | List[String] | | Which variant caller to use |
| - | output_dir | Path | Path to output directory |
......@@ -44,7 +44,7 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
Specific configuration options additional to Basty are:
| configNamespace | Name | Type | Default | Function |
| namespace | Name | Type | Default | Function |
| --------- | ---- | ---- | ------- | -------- |
| raxml | seed | Integer | 12345 | RAxML Random seed|
| raxml | raxml_ml_model | String | GTRGAMMAX | RAxML model |
......
......@@ -161,7 +161,7 @@ The other mode, `library_variantcalling`, will call simultaneously call all libr
The config for these therefore is:
| configNamespace | Name | Type | Default | Function |
| namespace | Name | Type | Default | Function |
| ----------- | ---- | ---- | ------- | -------- |
| shiva | multisample_variantcalling | Boolean | true | Default, multisample calling |
| shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |
......
......@@ -20,7 +20,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
qscript =>
def this() = this(null)
/** Make variantcalling configNamespace, this with the gatk modes in there */
/** Make variantcalling namespace, this with the gatk modes in there */
override def makeVariantcalling(multisample: Boolean = false) = {
if (multisample) new ShivaVariantcalling(qscript) {
override def namePrefix = "multisample"
......
......@@ -131,11 +131,11 @@ trait BastyTrait extends MultiSampleQScript {
raxmlMl.p = Some(seed)
raxmlMl.n = outputName + "_ml"
raxmlMl.w = dirSufixRaxml
raxmlMl.N = config("ml_runs", default = 20, configNamespace = "raxml")
raxmlMl.N = config("ml_runs", default = 20, namespace = "raxml")
add(raxmlMl)
val r = new scala.util.Random(seed)
val numBoot = config("boot_runs", default = 100, configNamespace = "raxml").asInt
val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
val bootList = for (t <- 0 until numBoot) yield {
val raxmlBoot = new Raxml(this)
raxmlBoot.input = variants
......
......@@ -19,7 +19,7 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
/** Biopet commandline class for java based programs */
trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunction {
executable = config("java", default = "java", configNamespace = "java", freeVar = false)
executable = config("java", default = "java", namespace = "java", freeVar = false)
javaGCThreads = config("java_gc_threads", default = 4)
javaGCHeapFreeLimit = config("java_gc_heap_freelimit", default = 10)
......
......@@ -31,7 +31,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
@Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
@Argument(doc = "Config values, value should be formatted like 'key=value' or 'configNamespace:configNamespace:key=value'", fullName = "config_value", shortName = "cv", required = false)
@Argument(doc = "Config values, value should be formatted like 'key=value' or 'namespace:namespace:key=value'", fullName = "config_value", shortName = "cv", required = false)
val configValues: List[String] = Nil
/** Output directory of pipeline */
......
......@@ -70,7 +70,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
def libDir = new File(sampleDir, "lib_" + libId)
lazy val libTags: Map[String, Any] =
config("tags", default = Map(), freeVar = false, configNamespace = libId, path = List("samples", sampleId, "libraries"))
config("tags", default = Map(), freeVar = false, namespace = libId, path = List("samples", sampleId, "libraries"))
def sampleId = sample.sampleId
......@@ -91,7 +91,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
lazy val sampleTags: Map[String, Any] =
config("tags", default = Map(), freeVar = false, configNamespace = sampleId, path = List("samples"))
config("tags", default = Map(), freeVar = false, namespace = sampleId, path = List("samples"))
lazy val gender = {
val g: Option[String] = sampleTags.get("gender").map(_.toString)
......
......@@ -24,7 +24,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
@Input(doc = "Python script", required = false)
var pythonScript: File = _
executable = config("exe", default = "python", configNamespace = "python", freeVar = false)
executable = config("exe", default = "python", namespace = "python", freeVar = false)
protected var pythonScriptName: String = _
......
......@@ -40,7 +40,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
var output: File = null
executable = config("exe", default = "fastqc")
var javaExe: String = config("exe", default = "java", configNamespace = "java", freeVar = false)
var javaExe: String = config("exe", default = "java", namespace = "java", freeVar = false)
var kmers: Option[Int] = config("kmers")
var quiet: Boolean = config("quiet", default = false)
var noextract: Boolean = config("noextract", default = false)
......
......@@ -32,7 +32,7 @@ import scala.io.Source
*/
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
executable = config("exe", configNamespace = "perl", default = "perl")
executable = config("exe", namespace = "perl", default = "perl")
var vepScript: String = config("vep_script")
@Input(doc = "input VCF", required = true)
......
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
abstract class Bcftools extends BiopetCommandLineFunction with Version {
override def subPath = "bcftools" :: super.subPath
executable = config("exe", default = "bcftools", configNamespace = "bcftools", freeVar = false)
executable = config("exe", default = "bcftools", namespace = "bcftools", freeVar = false)
def versionCommand = executable
def versionRegex = """Version: (.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
/** General abstract class for bedtools extensions */
abstract class Bedtools extends BiopetCommandLineFunction with Version {
override def subPath = "bedtools" :: super.subPath
executable = config("exe", default = "bedtools", configNamespace = "bedtools")
executable = config("exe", default = "bedtools", namespace = "bedtools")
def versionCommand = executable + " --version"
def versionRegex = """bedtools (.*)""".r
}
\ No newline at end of file
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
var executable: String = config("java", default = "java", configNamespace = "java", freeVar = false)
var executable: String = config("java", default = "java", namespace = "java", freeVar = false)
override def subPath = "gatk" :: super.subPath
......
......@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
* Created by wyleung on 5-1-15
*/
abstract class IGVTools extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "igvtools", configNamespace = "igvtools", freeVar = false)
executable = config("exe", default = "igvtools", namespace = "igvtools", freeVar = false)
def versionCommand = executable + " version"
def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
override def versionExitcode = List(0)
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
* Created by sajvanderzeeuw on 12/19/14.
*/
abstract class Macs2 extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "macs2", configNamespace = "macs2", freeVar = false)
executable = config("exe", default = "macs2", namespace = "macs2", freeVar = false)
def versionCommand = executable + " --version"
def versionRegex = """macs2 (.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
* manwe [subcommand]
*/
abstract class Manwe extends BiopetCommandLineFunction {
executable = config("exe", default = "manwe", configNamespace = "manwe")
executable = config("exe", default = "manwe", namespace = "manwe")
var manweConfig: File = createManweConfig(None)
......
......@@ -24,7 +24,7 @@ abstract class Sambamba extends BiopetCommandLineFunction with Version {
override def subPath = "sambamba" :: super.subPath
executable = config("exe", default = "sambamba", configNamespace = "sambamba", freeVar = false)
executable = config("exe", default = "sambamba", namespace = "sambamba", freeVar = false)
def versionCommand = executable
def versionRegex = """sambamba v(.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
/** General class for samtools extensions */
abstract class Samtools extends BiopetCommandLineFunction with Version {
override def subPath = "samtools" :: super.subPath
executable = config("exe", default = "samtools", configNamespace = "samtools", freeVar = false)
executable = config("exe", default = "samtools", namespace = "samtools", freeVar = false)
def versionCommand = executable
def versionRegex = """Version: (.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -319,7 +319,7 @@ object ConfigUtils extends Logging {
val exist = valueExists(value)
if (!exist)
Logging.addError("Value does not exist but is required, key: " + value.requestIndex.key +
" configNamespace: " + value.requestIndex.module,
" namespace: " + value.requestIndex.module,
if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null)
exist
}
......
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