Commit 3b1b89af authored by akaljuvee's avatar akaljuvee
Browse files

forcing the user to set the 'maxins' parameter

parent 6e1f2a48
...@@ -74,6 +74,9 @@ class Bowtie(val parent: Configurable) ...@@ -74,6 +74,9 @@ class Bowtie(val parent: Configurable)
s"No index files found for bowtie in: $indexDir with basename: $basename") s"No index files found for bowtie in: $indexDir with basename: $basename")
} }
} }
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.")
}
} }
/** return commandline to execute */ /** return commandline to execute */
......
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