Commit bae8c53d authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-BIOPET-493' into 'develop'

Fixing Biopet-493



See merge request !505
parents 32ddf7a8 3c73be57
...@@ -204,7 +204,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -204,7 +204,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName) fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats") fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
val pipe = new BiopetFifoPipe(this, fqSync :: Nil) with Summarizable { val pipe = new BiopetFifoPipe(this, fqSync :: qcCmdR1.jobs ::: qcCmdR2.jobs) with Summarizable {
override def configNamespace = "qc_cmd" override def configNamespace = "qc_cmd"
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
...@@ -233,6 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -233,6 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
pipe.deps ::= fastqcR1.output pipe.deps ::= fastqcR1.output
pipe.deps ::= fastqcR2.output pipe.deps ::= fastqcR2.output
pipe.deps ::= R1_in
pipe.deps ::= R2_in.get
pipe.isIntermediate = !keepQcFastqFiles pipe.isIntermediate = !keepQcFastqFiles
addSummarizable(pipe, "qc_cmd") addSummarizable(pipe, "qc_cmd")
add(pipe) add(pipe)
......
...@@ -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) logger.warn(s"Input R1 is a empty file: $inputR1")
inputR2.foreach(r => if (r.exists() && r.length() == 0) logger.warn(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(_))
...@@ -171,7 +173,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -171,7 +173,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val chunkSize: String = config("chunksize", default = "5G") val chunkSize: String = config("chunksize", default = "5G")
val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3 val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3
else inputR1.length else inputR1.length
numberChunks = Option(ceil(filesize.toDouble / textToSize(chunkSize)).toInt) numberChunks = Some(ceil(filesize.toDouble / textToSize(chunkSize)).toInt)
if (numberChunks == Some(0)) numberChunks = Some(1)
} }
} }
logger.debug("Chunks: " + numberChunks.getOrElse(1)) logger.debug("Chunks: " + numberChunks.getOrElse(1))
......
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