Commit 99cc75c4 authored by bow's avatar bow
Browse files

Merge branch 'patch-toucan' into 'develop'

Patch toucan

This enables to `--fork` command of the VEP to actually run with Biopet's `-qsub` command.

See merge request !126
parents 4387eae8 7059cf76
......@@ -119,7 +119,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var cache_region_size: Option[String] = config("cache_region_size")
// Numeric args
var fork: Option[Int] = config("fork")
override val defaultThreads: Int = config("fork", default = 2)
var cache_version: Option[Int] = config("cache_version")
var freq_freq: Option[Float] = config("freq_freq")
var port: Option[Int] = config("port")
......@@ -229,7 +229,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--build", build) +
optional("--compress", compress) +
optional("--cache_region_size", cache_region_size) +
optional("--fork", fork) +
optional("--fork", threads) +
optional("--cache_version", cache_version) +
optional("--freq_freq", freq_freq) +
optional("--port", port) +
......
......@@ -33,11 +33,16 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
var outputVCF: File = null
var mode: String = config("mode", default = "explode")
var doNotRemove: Boolean = config("donotremove", default = false)
memoryLimit = Some(1.0)
override val defaultVmem = "4G"
override def commandLine = super.commandLine +
required("-I", inputVCF) +
required("-O", outputVCF) +
required("-m", mode)
required("-m", mode) +
conditional(doNotRemove, "--do-not-remove")
}
object VEPNormalizer extends ToolCommand {
......
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