@@ -282,7 +282,8 @@ class Tophat(val parent: Configurable)
.exists(_.endsWith(".bt2")))
thrownewIllegalArgumentException("No bowtie2 index found for tophat")
if(R2.nonEmpty&&mateInnerDist.isEmpty){
logger.warn("The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
logger.warn(
"The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
@@ -75,7 +75,8 @@ class Bowtie(val parent: Configurable)
}
}
if(R2.nonEmpty&&maxins.isEmpty){
Logging.addError("The parameter 'maxins' that specifies the maximum allowed insert size, is missing in the configuration. Please note that Bowtie won't align reads coming from inserts longer than this value.")
Logging.addError(
"The parameter 'maxins' that specifies the maximum allowed insert size, is missing in the configuration. Please note that Bowtie won't align reads coming from inserts longer than this value.")