From 5acf703f8d16929a723e2be24bdd7ba828e4283c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 15:43:06 +0100
Subject: [PATCH] Remove chunked files from summary
---
.../scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala | 4 +---
.../main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala | 9 +--------
.../lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala | 5 +----
4 files changed, 4 insertions(+), 16 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
index a8bf55177..556f8639f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
@@ -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 {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index f47eeb300..e69134b93 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -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.
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index 55f964451..e9f6bd492 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -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 {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
index dc63f70bf..ec452f187 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
@@ -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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