Commit 6dcb0071 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added Summarize flexiprep wrapper

parent a19aa261
package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import org.broadinstitute.sting.commandline._
import java.io.File
class Summarize(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "flexiprep_sumarize"
val config: Config = globalConfig.getAsConfig(analysisName)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
setPythonScript("summarize_flexiprep.py", "scripts/")
@Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
@Output(doc="Output file", shortName="out", required=true) var out: File = _
var samplea: String = _
var sampleb: String = _
var runDir: String = _
var samplename: String = _
var trim: Boolean = true
var clip: Boolean = true
def commandLine = {
var mode: String = ""
if (clip) mode += "clip"
if (trim) mode += "trim"
if (mode.isEmpty) mode = "none"
getPythonCommand +
optional("--run-dir", runDir) +
optional("--sampleb", sampleb) +
required(samplename) +
required(mode) +
required(samplea) +
required(out)
}
}
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