Commit 5a635225 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added plots to outputFiles

parent 273e70f5
......@@ -19,6 +19,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{ File, FileNotFoundException }
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.Output
import scala.io.Source
......@@ -167,8 +168,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
ConfigUtils.mapToJson(outputMap)
}
@Output
var outputFiles: List[File] = Nil
def summaryFiles: Map[String, File] = {
Map("plot_duplication_levels" -> ("Images" + File.separator + "duplication_levels.png"),
val outputFiles = Map("plot_duplication_levels" -> ("Images" + File.separator + "duplication_levels.png"),
"plot_kmer_profiles" -> ("Images" + File.separator + "kmer_profiles.png"),
"plot_per_base_gc_content" -> ("Images" + File.separator + "per_base_gc_content.png"),
"plot_per_base_n_content" -> ("Images" + File.separator + "per_base_n_content.png"),
......@@ -178,7 +182,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
"plot_per_sequence_quality" -> ("Images" + File.separator + "per_sequence_quality.png"),
"plot_sequence_length_distribution" -> ("Images" + File.separator + "sequence_length_distribution.png"),
"fastqc_data" -> ("fastqc_data.txt"))
.map(x => (x._1 -> new File(outputDir, x._2))) ++ Map("fastq_file" -> this.fastqfile)
.map(x => (x._1 -> new File(outputDir, x._2)))
outputFiles.foreach(this.outputFiles :+= _._2)
outputFiles ++ Map("fastq_file" -> this.fastqfile)
}
def summaryData: Map[String, Any] = Map("version" -> getVersion)
......
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