Commit 3e9b759b authored by Sander Bollen's avatar Sander Bollen
Browse files

autogenerated styles

parent 23e0dbe1
......@@ -94,7 +94,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
}
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
......
package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{Output, Argument}
import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
/**
* Created by ahbbollen on 23-9-15.
......@@ -17,7 +16,7 @@ abstract class Manwe extends BiopetCommandLineFunction {
override def defaultCoreMemory = 2.0
override def defaultThreads = 1
@Argument(doc="Path to manwe config file containing your database settings", required = true)
@Argument(doc = "Path to manwe config file containing your database settings", required = true)
var manweConfig: Option[File] = config("manwe_config")
@Output(doc = "the output file")
......@@ -25,15 +24,15 @@ abstract class Manwe extends BiopetCommandLineFunction {
var manweHelp: Boolean = false
def subCommand : String
def subCommand: String
final def cmdLine = {
required(executable) +
subCommand +
required("-c", manweConfig) +
conditional(manweHelp, "-h") +
" > " +
required(output)
subCommand +
required("-c", manweConfig) +
conditional(manweHelp, "-h") +
" > " +
required(output)
}
/**
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Argument}
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
/**
* Created by ahbbollen on 24-9-15.
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Created by ahbbollen on 24-9-15.
......@@ -21,11 +21,8 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
def subCommand = {
required("annotate-vcf") + required(vcf) +
conditional(alreadyUploaded, "-u") +
repeat("-q", queries)
conditional(alreadyUploaded, "-u") +
repeat("-q", queries)
}
}
......@@ -16,9 +16,7 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
def subCommand = {
required("data-sources") + required("annotate") +
required(uri) + repeat("-q", queries)
required(uri) + repeat("-q", queries)
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -15,10 +15,8 @@ class ManweDataSourcesList(val root: Configurable) extends Manwe {
def subCommand = {
required("data-sources") + required("list") +
optional("-u", user)
optional("-u", user)
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -11,11 +11,11 @@ import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
class ManweDataSourcesShow(val root: Configurable) extends Manwe {
@Argument(doc = "uri of data source")
var uri: Option[String] = _
var uri: Option[String] = _
def subCommand = {
required("data-sources") + required("show") +
required(uri)
required(uri)
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -15,8 +15,7 @@ class ManweSamplesActivate(val root: Configurable) extends Manwe {
def subCommand = {
required("samples") + required("activate") +
required(uri)
required(uri)
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -21,10 +21,7 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
def subCommand = {
required("samples") + required("add") + required(name) +
optional("-s", poolSize) + repeat("-g", group)
optional("-s", poolSize) + repeat("-g", group)
}
}
......@@ -3,15 +3,14 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
*/
class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
@Argument(doc= "uri to sample to annotate")
@Argument(doc = "uri to sample to annotate")
var uri: Option[String] = _
@Argument(doc = "Annotation queries")
......@@ -19,10 +18,7 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
def subCommand = {
required("samples") + required("annotate-variations") +
required(uri) + repeat("-q", queries)
required(uri) + repeat("-q", queries)
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -39,18 +39,14 @@ class ManweSamplesImport(val root: Configurable) extends Manwe {
var preferLikelihood: Boolean = false
@Argument(doc = "Pool size")
var poolSize : Option[Int] = _
var poolSize: Option[Int] = _
def subCommand = {
required("samples") + required("import") + required(name) +
repeat("-g", group) + repeat("--vcf", vcfs) + repeat("--bed", beds) +
optional("-s", poolSize) + conditional(alreadyUploaded, "-u") +
conditional(public, "-p") + conditional(preferLikelihood, "-l") +
conditional(noCoverage, "--no-coverage-profile")
repeat("-g", group) + repeat("--vcf", vcfs) + repeat("--bed", beds) +
optional("-s", poolSize) + conditional(alreadyUploaded, "-u") +
conditional(public, "-p") + conditional(preferLikelihood, "-l") +
conditional(noCoverage, "--no-coverage-profile")
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -20,8 +20,7 @@ class ManweSamplesImportBed(val root: Configurable) extends Manwe {
@Argument(doc = "path to VCF file to upload")
var bed: File = _
@Argument(doc = "flag if data is already uploaded?")
// TODO: What is the use of this flag even? We're specifically uploading with this command
@Argument(doc = "flag if data is already uploaded?") // TODO: What is the use of this flag even? We're specifically uploading with this command
var alreadyUploaded: Boolean = false
def subCommand = {
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......@@ -20,8 +20,7 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
@Argument(doc = "path to VCF file to upload")
var vcf: File = _
@Argument(doc = "flag if data is already uploaded?")
// TODO: What is the use of this flag even? We're specifically uploading with this command
@Argument(doc = "flag if data is already uploaded?") // TODO: What is the use of this flag even? We're specifically uploading with this command
var alreadyUploaded: Boolean = false
@Argument(doc = "Flag when to prefer genotype likelihoods")
......@@ -29,8 +28,8 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
def subCommand = {
required("samples") + required("import-vcf") +
required(uri) + required(vcf) +
conditional(alreadyUploaded, "-u") + conditional(preferLikelihoods, "-l")
required(uri) + required(vcf) +
conditional(alreadyUploaded, "-u") + conditional(preferLikelihoods, "-l")
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 23-9-15.
......@@ -20,12 +20,7 @@ class ManweSamplesList(val root: Configurable) extends Manwe {
def subCommand = {
required("samples") + required("list") + optional("-u", user) +
repeat("-g", group) + conditional(onlyPublic, "-p")
repeat("-g", group) + conditional(onlyPublic, "-p")
}
}
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.manwe
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by ahbbollen on 24-9-15.
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment