Commit 18bc6d01 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed sample and library check

parent 63029298
......@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.IoUtils._
import nl.lumc.sasc.biopet.extensions.tools.{ ValidateFastq, SeqStat, FastqSync }
import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat, ValidateFastq }
import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......@@ -74,10 +74,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Function that's need to be executed before the script is accessed */
def init() {
require(outputDir != null, "Missing output directory on flexiprep module")
require(inputR1 != null, "Missing input R1 on flexiprep module")
require(sampleId != null, "Missing sample ID on flexiprep module")
require(libId != null, "Missing library ID on flexiprep module")
if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on flexiprep module")
if (libId == null || libId == None) Logging.addError("Missing library ID on flexiprep module")
paired = inputR2.isDefined
......
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