Analysis: building sortmerna index
Feature request
Add a rule to the installation workflow to build the index for the downloaded sortmerna FASTA files.
See the rule
sortmerna_databases_index here.This rule is not executed as databases.smk is not included in the main Snakefile.
Update
Since version 4.0, sortmerna does not have a command for creating the index files (see here), and the created index files are not named using the base names of the given FASTA files.
Since building the index files seems to be fast, and defining the expected base names is too cumbersome, the index files should be built by sortmerna when the main pipeline is being executed.
Use the code base from issue #33 (closed) (branch issue33).