Trimal module

[vagkaratzas]

Description of feature

1. As clipkit alternative for MSA trimming (C++ should be faster than python).
2. As strict clustering alternative instead of four mmseqs modules (-clusters argument now works properly), to keep representative sequences (whenever checking for redundancy).

Asked both trimal and clipkit repos to add a flag that also recalculates sequence start-end coords properly after timming ends-only.

• clipkit won't do that for now
• trimal might
• else need to create a local module (python or Rust code)

Also, add both clipkit/trimal (and downstream renumbering module if done locally) to the align_sequences subworkflow