Rule parameters: Catch/forbid user to set cutadapt's -m to zero
Currently the rule_config
contains a comment with warning about setting -m
to zero. However, this is not impressive enough. Moreover, if the rule_config
is omitted, cutadapt's default is -m 0
. This might lead to empty reads being included in the files, which in turn will cause STAR to fail. The general error messages will not be informative enough for inexperienced users, we should explicitly catch that case or prevent it all together.
Where to perform this check? Probably in def parse_rule_config
.