From 4ae1272297f78e875324357f4d6618eec314e8dc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 4 Sep 2015 22:15:07 +0200
Subject: [PATCH] Code style fix
---
.../biopet/pipelines/gentrap/Gentrap.scala | 30 +++++++++----------
.../biopet/pipelines/mapping/Mapping.scala | 8 ++---
.../sasc/biopet/pipelines/sage/Sage.scala | 26 ++++++++--------
3 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 624c71700..fd98850b4 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -101,22 +101,22 @@ class Gentrap(val root: Configurable) extends QScript
/** Default pipeline config */
override def defaults = Map(
- "gsnap" -> Map(
- "novelsplicing" -> 1,
- "batch" -> 4,
- "format" -> "sam"
- ),
- "cutadapt" -> Map("minimum_length" -> 20),
- // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
- "picard" -> Map(
- "programrecordid" -> "null"
- ),
- // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
- "mapping" -> Map(
- "skip_markduplicates" -> true,
- "skip_metrics" -> true
- )
+ "gsnap" -> Map(
+ "novelsplicing" -> 1,
+ "batch" -> 4,
+ "format" -> "sam"
+ ),
+ "cutadapt" -> Map("minimum_length" -> 20),
+ // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
+ "picard" -> Map(
+ "programrecordid" -> "null"
+ ),
+ // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
+ "mapping" -> Map(
+ "skip_markduplicates" -> true,
+ "skip_metrics" -> true
)
+ )
/** Adds output merge jobs for the given expression mode */
// TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index ea77b64ad..792411413 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -98,11 +98,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
override def defaults = Map(
- "gsnap" -> Map(
- "batch" -> 4,
- "format" -> "sam"
- )
+ "gsnap" -> Map(
+ "batch" -> 4,
+ "format" -> "sam"
)
+ )
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 056081a15..b6fde5b75 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -38,19 +38,19 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
override def defaults = Map(
"bowtie" -> Map(
- "m" -> 1,
- "k" -> 1,
- "best" -> true,
- "strata" -> true,
- "seedmms" -> 1
- ), "mapping" -> Map(
- "aligner" -> "bowtie",
- "skip_flexiprep" -> true,
- "skip_markduplicates" -> true
- ), "flexiprep" -> Map(
- "skip_clip" -> true,
- "skip_trim" -> true
- ), "strandSensitive" -> true
+ "m" -> 1,
+ "k" -> 1,
+ "best" -> true,
+ "strata" -> true,
+ "seedmms" -> 1
+ ), "mapping" -> Map(
+ "aligner" -> "bowtie",
+ "skip_flexiprep" -> true,
+ "skip_markduplicates" -> true
+ ), "flexiprep" -> Map(
+ "skip_clip" -> true,
+ "skip_trim" -> true
+ ), "strandSensitive" -> true
)
def summaryFile: File = new File(outputDir, "Sage.summary.json")
--
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