explanation of the naming convention in the config and pipeline when using bowtie2_mapping rule

[cokelaer]

bowtie2_mapping (and other rules) are dynamic rules. This means that we can use them several
times in a pipeline. To do so, we must set their name as follows:

exec(open(sequana.modules["bowtie2_mapping_dynamic"], "r").read())
include: bowtie2_mapping_dynamic("ref", manager)

So here the actual rule is called bowtie2_mapping_ref. However, in the rule itself, the expected name in the configuration file is bowtie2_mapping. Therefore, the config file should bowtie2_mapping and not bowtie2_mapping_ref./

[cokelaer]

I was wondering whether this is a bug in the rule itself, and yes it is:

I fixed the rule bowtie2_mapping to make it fully