Commit 8242e484 authored by Peter van 't Hof's avatar Peter van 't Hof

Added intermendiate tags

parent 0efd042b
...@@ -54,12 +54,14 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w ...@@ -54,12 +54,14 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz") swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz")
else flash.notCombinedR2 else flash.notCombinedR2
val keepFastaqFiles: Boolean = config("keep_fastq_files", default = false)
/** Pipeline itself */ /** Pipeline itself */
def biopetScript(): Unit = { def biopetScript(): Unit = {
flash.outputDirectory = new File(outputDir, "flash") flash.outputDirectory = new File(outputDir, "flash")
flash.fastqR1 = fastqR1 flash.fastqR1 = fastqR1
flash.fastqR2 = fastqR2 flash.fastqR2 = fastqR2
flash.isIntermediate = (forwardPrimers ::: reversePrimers).nonEmpty flash.isIntermediate = !keepFastaqFiles || (forwardPrimers ::: reversePrimers).nonEmpty
add(flash) add(flash)
if ((forwardPrimers ::: reversePrimers).nonEmpty) { if ((forwardPrimers ::: reversePrimers).nonEmpty) {
...@@ -67,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w ...@@ -67,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
cutadapt.fastqInput = flash.combinedFastq cutadapt.fastqInput = flash.combinedFastq
cutadapt.fastqOutput = this.combinedFastq cutadapt.fastqOutput = this.combinedFastq
cutadapt.statsOutput = swapExt(outputDir, cutadapt.fastqOutput, ".fastq.gz", ".stats") cutadapt.statsOutput = swapExt(outputDir, cutadapt.fastqOutput, ".fastq.gz", ".stats")
cutadapt.isIntermediate = !keepFastaqFiles
(forwardPrimers ::: reversePrimers).foreach(cutadapt.anywhere += _) (forwardPrimers ::: reversePrimers).foreach(cutadapt.anywhere += _)
add(cutadapt) add(cutadapt)
addSummarizable(cutadapt, "cutadapt") addSummarizable(cutadapt, "cutadapt")
......
...@@ -58,6 +58,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri ...@@ -58,6 +58,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
splitLib.input :+= fastqInput splitLib.input :+= fastqInput
splitLib.outputDir = new File(outputDir, "split_libraries_fastq") splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-")) sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
splitLib.isIntermediate = true
add(splitLib) add(splitLib)
val closedReference = new PickClosedReferenceOtus(this) val closedReference = new PickClosedReferenceOtus(this)
......
...@@ -51,6 +51,7 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript ...@@ -51,6 +51,7 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
splitLib.input :+= fastqInput splitLib.input :+= fastqInput
splitLib.outputDir = new File(outputDir, "split_libraries_fastq") splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-")) sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
splitLib.isIntermediate = true
add(splitLib) add(splitLib)
val openReference = new PickOpenReferenceOtus(this) val openReference = new PickOpenReferenceOtus(this)
......
...@@ -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
......
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