nf-core
[Update] PretextMap should take a fai file
Is your feature request related to a problem? Please describe
PretextMap will index the incoming fasta file, in many cases this file will already be generated and just needs to be visible to the process (it cannot be declared to the software).
In the cases of large genomes (I have a 25Gb Newt!) this will speed up the mapping process and waste less resources as we are not indexing again.
Describe the solution you'd like
Solution is proposed here https://github.com/sanger-tol/treeval/pull/283
This changes the fasta file path into a tuple containing the meta, fasta and fai.
Describe alternatives you've considered
No response
Additional context
This will require the module to also be updated to use NF-Test.
The module will not be updated to use the sanger container shown in the linked issue, this is temporary until we can access the main repo to update it properly and includes only an extra flag for buffer_memory manipulation.
