Commit ee8bfca5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fastqc now compatible to version 0.11.2

parent c5f4ca8b
......@@ -11,6 +11,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
var contaminants: File = _
@Input(doc = "Adapters", required = false)
var adapters: File = _
@Input(doc = "Fastq file", shortName = "FQ")
var fastqfile: File = _
......@@ -34,7 +37,14 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
this.checkExecutable
if (contaminants == null) {
val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
val defaultContams = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
val defaultContams = getVersion match {
case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
}
val defaultAdapters = getVersion match {
case "v0.11.2" => new File(fastqcDir + "/Configuration/adapter_list.txt")
case _ => null
}
contaminants = config("contaminants", default = defaultContams)
}
}
......@@ -43,6 +53,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
optional("--java", java_exe) +
optional("--threads", threads) +
optional("--contaminants", contaminants) +
optional("--adapters", adapters) +
optional("--kmers", kmers) +
conditional(nogroup, "--nogroup") +
conditional(noextract, "--noextract") +
......
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