Commit bf372d9a authored by bow's avatar bow
Browse files

Update imports style order

parent 02b571a4
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import scala.io.Source._
import scala.sys.process._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input fastq file")
var fastq_input: File = _
......@@ -73,4 +75,4 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
} else logger.warn("File : " + contams_file + " does not exist")
}
}
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import scala.sys.process._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
......@@ -48,4 +50,4 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
required(fastqfile) +
required(" > ", output, escape = false)
}
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import scala.io.Source._
import scala.sys.process._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "R1 input")
var input_R1: File = null
......@@ -73,4 +75,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
}
return null
}
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.fastq._
import scala.util.parsing.json._
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk._
import org.broadinstitute.gatk.queue.extensions.picard._
import org.broadinstitute.gatk.queue.function._
import scala.util.parsing.json._
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.fastq._
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
......
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("sync_paired_end_reads.py")
......@@ -34,4 +36,4 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
required(output_R2) +
" > " +
required(output_stats)
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
......@@ -25,4 +27,4 @@ class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction
" > " +
required(out)
}
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
......@@ -21,4 +23,4 @@ class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction
" > " +
required(out)
}
}
\ No newline at end of file
}
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
......
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class Summarize(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
......@@ -33,4 +35,4 @@ class Summarize(val root: Configurable) extends PythonCommandLineFunction {
required(samplea) +
required(out)
}
}
\ No newline at end of file
}
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