Commit 7c863726 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding ValidateFastq to flexiprep

parent 46599c3f
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
def toolObject = nl.lumc.sasc.biopet.tools.ValidateFastq
@Input(doc = "Input R1 fastq file", required = true)
var r1Fastq: File = _
@Input(doc = "Input R1 fastq file", required = false)
var r2Fastq: Option[File] = None
override def cmdLine = super.cmdLine +
required("-i", r1Fastq) +
optional("-j", r2Fastq)
}
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibrary
import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.IoUtils._
import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
import nl.lumc.sasc.biopet.extensions.tools.{ValidateFastq, SeqStat, FastqSync}
import org.broadinstitute.gatk.queue.QScript
......@@ -114,6 +114,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable(fastqc_R1, "fastqc_R1")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
val validateFastq = new ValidateFastq(this)
validateFastq.r1Fastq = input_R1
validateFastq.r2Fastq = input_R2
validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
add(validateFastq)
if (paired) {
fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
add(fastqc_R2)
......
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