Commit 94d9ba32 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch seqstat to init jobs

parent 37e92018
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.tools.{SeqStat, FastqSync}
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......@@ -131,6 +131,18 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable(fastqc_R2, "fastqc_R2")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
}
val seqstat_R1 = SeqStat(this, input_R1, outputDir)
seqstat_R1.isIntermediate = true
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
if (paired) {
val seqstat_R2 = SeqStat(this, input_R2.get, outputDir)
seqstat_R2.isIntermediate = true
add(seqstat_R2)
addSummarizable(seqstat_R2, "seqstat_R2")
}
}
//TODO: Refactor need to combine all this functions
......@@ -174,20 +186,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
deps_R2 ::= R2.get
}
val seqstat_R1 = SeqStat(this, R1, outDir)
seqstat_R1.isIntermediate = true
seqstat_R1.deps = deps_R1
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
if (paired) {
val seqstat_R2 = SeqStat(this, R2.get, outDir)
seqstat_R2.isIntermediate = true
seqstat_R2.deps = deps_R2
add(seqstat_R2)
addSummarizable(seqstat_R2, "seqstat_R2")
}
if (!skipClip) { // Adapter clipping
val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment