Commit 9be7a784 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Option to skip summary

parent bd29df9d
......@@ -27,6 +27,9 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
@Argument(doc="Skip Clip fastq files", shortName="skipclip", required=false)
var skipClip: Boolean = false
@Argument(doc="Skip summary", shortName="skipsummary", required=false)
var skipSummary: Boolean = false
var paired: Boolean = (input_R2 != null)
var R1_ext: String = _
var R2_ext: String = _
......@@ -223,16 +226,18 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
if (!skipSummary) {
val summarize = new Summarize(this)
summarize.runDir = outputDir
summarize.samplea = R1_name
if (paired) summarize.sampleb = R2_name
summarize.samplename = R1_name
summarize.clip = !skipClip
summarize.trim = !skipTrim
summarize.out = new File(outputDir + R1_name + ".summary.json")
for ((k,v) <- outputFiles) summarize.deps +:= v
add(summarize)
summarize.runDir = outputDir
summarize.samplea = R1_name
if (paired) summarize.sampleb = R2_name
summarize.samplename = R1_name
summarize.clip = !skipClip
summarize.trim = !skipTrim
summarize.out = new File(outputDir + R1_name + ".summary.json")
for ((k,v) <- outputFiles) summarize.deps +:= v
add(summarize)
}
}
def runFastqc(fastqfile:File, outDir:String) : Fastqc = {
......
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