Add MMseqs makepaddedseqdb

[nbtm-sh]

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Description

This PR adds support for MMseqs makepaddedseqdb, used for GPU accelerated searches. It takes in an existing MMseqs database, and outputs a padded database in a similar format.

[keiran-rowell-unsw]

Small changes to fix. Would like another non-fresh nf-core maintainer to approve if they have greater knowledge of module consistency

[Joon-Klaps]

Couple of minor issues, nice addition.

[Joon-Klaps]

Don't think you need to make an alias here, you don't have any other MMSEQS_CREATEDB modules in your setup.

[nbtm-sh]

You're right. Removed

[Joon-Klaps]

Suprised these are consistent but that's good!

[Joon-Klaps]

This will not always give the wanted results.

MMseqs allows to have multiple databases in a single directory. To avoid this we have implemented this (ugly) find command so users can specify if necessary which database to use here.

# Extract files with specified args based suffix | remove suffix | isolate longest common substring of files
    DB_TARGET_PATH_NAME=\$(find -L "${db_target}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' 

[Joon-Klaps]

change all to prefix

[nbtm-sh]

@Joon-Klaps thanks for the feedback and commit suggestions. I'd also like to apologise for my messy commit history. I believe I have implemented all changes you have suggested, and have updated meta.yml and tests accordingly. All tests are passing on my end.

Do let me know if any extra changes are needed or I've missed any suggestions.

P.S, I noticed that there is a maintainer field in the meta.yml file. Would you like me to maintain this module going forward?

[Joon-Klaps]

Hi @nbtm-sh, Looks great!
Have to double check if all tests are passing correctly, check if you can update your local branch to be in sync with the master branch as some modules you didn't touch are being ran (which typically means, your local fork is outdated).

You are free to add yourself as a maintainer of the module, if you don't want to, no pressure. This module will be kept up to date as it's part of the mmseqs suite.

[nbtm-sh]

Hey @Joon-Klaps, thanks for that.

I'm happy to maintain the module going forward. I have synced this fork with the upstream and added myself to the yaml file. Let me know if anything else needs to be changed.

Cheers

[keiran-rowell-unsw]

LGTM, Joon's review was great improvement.