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 ...@@ -19,6 +19,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{ File, FileNotFoundException } import java.io.{ File, FileNotFoundException }
import nl.lumc.sasc.biopet.core.summary.Summarizable import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.Output
import scala.io.Source import scala.io.Source
...@@ -167,8 +168,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r ...@@ -167,8 +168,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
ConfigUtils.mapToJson(outputMap) ConfigUtils.mapToJson(outputMap)
} }
@Output
var outputFiles: List[File] = Nil
def summaryFiles: Map[String, File] = { 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_kmer_profiles" -> ("Images" + File.separator + "kmer_profiles.png"),
"plot_per_base_gc_content" -> ("Images" + File.separator + "per_base_gc_content.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"), "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 ...@@ -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_per_sequence_quality" -> ("Images" + File.separator + "per_sequence_quality.png"),
"plot_sequence_length_distribution" -> ("Images" + File.separator + "sequence_length_distribution.png"), "plot_sequence_length_distribution" -> ("Images" + File.separator + "sequence_length_distribution.png"),
"fastqc_data" -> ("fastqc_data.txt")) "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) def summaryData: Map[String, Any] = Map("version" -> getVersion)
......
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