From 5a635225a1b7b73e27f3ad3f446c142e34eec068 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 11:31:43 +0100
Subject: [PATCH] Added plots to outputFiles
---
.../sasc/biopet/pipelines/flexiprep/Fastqc.scala | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 73b2288f0..c7554f0e4 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -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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