Commit 86ecb782 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a check on empty files

parent 24a1b29e
...@@ -19,11 +19,11 @@ import java.util.Date ...@@ -19,11 +19,11 @@ import java.util.Date
import nl.lumc.sasc.biopet.core._ import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 } import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse } import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam } import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions._ import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig ...@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import nl.lumc.sasc.biopet.utils.textToSize import nl.lumc.sasc.biopet.utils.{Logging, textToSize}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
...@@ -150,9 +150,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -150,9 +150,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Will be executed before script */ /** Will be executed before script */
def init() { def init() {
require(outputDir != null, "Missing output directory on mapping module") require(outputDir != null, "Missing output directory on mapping module")
require(inputR1 != null, "Missing output directory on mapping module") require(inputR1 != null, "Missing inputR1 on mapping module")
require(sampleId.isDefined, "Missing sample ID on mapping module") require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module") require(libId.isDefined, "Missing library ID on mapping module")
if (inputR1.exists() && inputR1.length() == 0) Logging.addError(s"Input R1 is a empty file: $inputR1")
inputR2.foreach(r => if (r.exists() && r.length() == 0) Logging.addError(s"Input R2 is a empty file: $r"))
inputFiles :+= new InputFile(inputR1) inputFiles :+= new InputFile(inputR1)
inputR2.foreach(inputFiles :+= new InputFile(_)) inputR2.foreach(inputFiles :+= new InputFile(_))
......
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