From c7b0c4152f5d01c05a7a067fe90202418017ec9b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 May 2016 09:32:14 +0200
Subject: [PATCH] Addec config option to disable merging of countfiles
---
.../gentrap/measures/Measurement.scala | 25 ++++++++++++-------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
index b07d295a8..8f470ee06 100644
--- a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
+++ b/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -29,6 +29,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
/**
* Method to add a bamFile to the pipeline
+ *
* @param id Unique id used for this bam file, most likely to be a sampleName
* @param file Location of the bam file
*/
@@ -51,6 +52,8 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require(bamFiles.nonEmpty)
}
+ lazy val mergeCountFiles: Boolean = config("merge_count_files", default = true)
+
private var extraSummaryFiles: Map[String, File] = Map()
def addMergeTableJob(countFiles: List[File],
@@ -58,18 +61,22 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
name: String,
fileExtension: String,
args: MergeArgs = mergeArgs): Unit = {
- add(MergeTables(this, countFiles, outputFile,
- args.idCols, args.valCol, args.numHeaderLines, args.fallback, fileExtension = Some(fileExtension)))
- extraSummaryFiles += s"${name}_table" -> outputFile
+ if (mergeCountFiles) {
+ add(MergeTables(this, countFiles, outputFile,
+ args.idCols, args.valCol, args.numHeaderLines, args.fallback, fileExtension = Some(fileExtension)))
+ extraSummaryFiles += s"${name}_table" -> outputFile
+ }
}
def addHeatmapJob(countTable: File, outputFile: File, name: String, countType: Option[String] = None): Unit = {
- val job = new PlotHeatmap(qscript)
- job.input = countTable
- job.output = outputFile
- job.countType = countType
- add(job)
- extraSummaryFiles += s"${name}_heatmap" -> outputFile
+ if (mergeCountFiles) {
+ val job = new PlotHeatmap(qscript)
+ job.input = countTable
+ job.output = outputFile
+ job.countType = countType
+ add(job)
+ extraSummaryFiles += s"${name}_heatmap" -> outputFile
+ }
}
/** Must return a map with used settings for this pipeline */
--
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