Commit 8bed40ff authored by bow's avatar bow
Browse files

Fix missing wiggle jobs

parent 57622630
......@@ -31,6 +31,7 @@ import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
import nl.lumc.sasc.biopet.extensions.picard.{ CollectRnaSeqMetrics, SortSam, MergeSamFiles }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
......@@ -725,6 +726,10 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
addSummaryQScript(m)
case None => ;
}
// add bigwig output, also per-strand when possible
addAll(Bam2Wig(qscript, alnFile).functions)
alnFilePlusStrand.collect { case f => addAll(Bam2Wig(qscript, f).functions) }
alnFileMinusStrand.collect { case f => addAll(Bam2Wig(qscript, f).functions) }
// add strand-specific jobs if defined
alnPlusStrandJobs.foreach(_.addAllJobs())
alnMinusStrandJobs.foreach(_.addAllJobs())
......@@ -771,6 +776,9 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def collectRnaSeqMetricsJob: CollectRnaSeqMetrics =
makeCollectRnaSeqMetricsJob(alnFile, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
/** Wiggle track job */
private lazy val bam2wigModule: Bam2Wig = Bam2Wig(qscript, alnFile)
/** Per-library mapping job */
def mappingJob: Mapping = {
val job = new Mapping(qscript)
......@@ -787,6 +795,8 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def addJobs(): Unit = {
// create per-library alignment file
addAll(mappingJob.functions)
// add bigwig track
addAll(bam2wigModule.functions)
// create RNA metrics job
add(collectRnaSeqMetricsJob)
addSummarizable(collectRnaSeqMetricsJob, "rna_metrics")
......
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