Commit a19aa261 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added Seqstat wrapper

parent 4eb2d994
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 Seqstat(val globalConfig: Config) extends CommandLineFunction with Python {
def this() = this(new Config(Map()))
analysisName = "seqstat"
val config: Config = globalConfig.getAsConfig(analysisName)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
setPythonScript("seq_stat.py", "scripts/")
@Input(doc="Fastq input", shortName="fastqc", required=true) var input_fastq: File = _
@Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
@Output(doc="Output file", shortName="out", required=true) var out: File = _
var fmt: String = _
def commandLine = {
getPythonCommand +
optional("--fmt", fmt) +
required("-o", out) +
required(input_fastq)
}
}
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