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biopet.biopet
Commit 35bd64d6 authored by Peter van 't Hof's avatar Peter van 't Hof
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Make output name required

parent e7437482
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Showing with 2 additions and 8 deletions
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @ 35bd64d6
...@@ -23,10 +23,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip ...@@ -23,10 +23,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
def init(): Unit = { def init(): Unit = {
require(fastqR1 != null) require(fastqR1 != null)
if (outputName == null) outputName = fastqR1.getName require(outputName != null)
.stripSuffix(".gz")
.stripSuffix(".fq")
.stripSuffix(".fastq")
} }
def biopetScript(): Unit = { def biopetScript(): Unit = {
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @ 35bd64d6
...@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi ...@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
def init(): Unit = { def init(): Unit = {
require(fastqR1 != null) require(fastqR1 != null)
if (outputName == null) outputName = fastqR1.getName require(outputName != null)
.stripSuffix(".gz")
.stripSuffix(".fq")
.stripSuffix(".fastq")
} }
lazy val krakenConvertToFasta: Boolean = config("kraken_discard_quality", default = false) lazy val krakenConvertToFasta: Boolean = config("kraken_discard_quality", default = false)
......
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