Commit 5acf703f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove chunked files from summary

parent 1f620a44
......@@ -51,9 +51,7 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction with Sum
ConfigUtils.any2map(map.getOrElse("stats", Map()))
}
def summaryFiles: Map[String, File] = {
Map("fastq" -> input)
}
def summaryFiles: Map[String, File] = Map()
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
(v1, v2) match {
......
......@@ -65,14 +65,7 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
required("-p", outputFastq2) + " > " +
required(outputStats)
def summaryFiles: Map[String, File] = {
Map("refFastq" -> refFastq,
"inputFastq1" -> inputFastq1,
"inputFastq2" -> inputFastq2,
"outputFastq1" -> outputFastq1,
"outputFastq2" -> outputFastq2
)
}
def summaryFiles: Map[String, File] = Map()
def summaryData: Map[String, Any] = {
val regex = new Regex("""Filtered (\d*) reads from first read file.
......
......@@ -85,7 +85,7 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
}
}
def summaryFiles: Map[String, File] = Map("input" -> fastq_input, "output" -> fastq_output)
def summaryFiles: Map[String, File] = Map()
}
object Cutadapt {
......
......@@ -62,8 +62,5 @@ class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(r
}
}
def summaryFiles: Map[String, File] = {
Map("input_R1" -> input_R1, "output_R1" -> output_R1) ++
(if (input_R2 != null) Map("input_R2" -> input_R2, "output_R2" -> output_R2) else Map())
}
def summaryFiles: Map[String, File] = Map()
}
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