Eukulele

Update to prior release to add tab removal step for `phylodb` database. In this release, we address several long-standing issues in ``EUKulele`` and add a new feature.

- Changes the name of the `pident` column to reflect that it is really the best quality score
- Fixed issues related to errors of "MissingFromTaxDict" (https://github.com/AlexanderLabWHOI/EUKulele/issues/60)
- Allowed gzipped database fastas to be used (https://github.com/nf-core/metatdenovo/issues/256)
- Newest version of EukProt now downloads with `EUKulele` and EukProt protein map bugs have been resolved; gzipped version of fasta also downloads (https://github.com/AlexanderLabWHOI/EUKulele/issues/66)
- Fixed database download issues for GTDB add-on
- Updated calls to `append` with calls to `concat` (`pandas`)
- Fixed some instances of spaces being introduced to taxonomy strings during parsing

New feature:
- Added a flag, `--create_euk_fasta`, to dump a fasta file of eukaryotic sequences after a `EUKulele` run (https://github.com/AlexanderLabWHOI/EUKulele/issues/35)

Updating README_db file, making changes to error reporting, sending draft release to bioconda to fix containerization issue

In this release, we

- Updated URLs for use of GTDB as a reference database
- Revised code for use of `--threads` parameter within `DIAMOND`
- Changed dependencies

Very small update to v2.0.1 for integration purposes.

Changed:
- added quotes to URLs in wget calls to deal with wget utility type

In this release, we address several long-standing issues in ``EUKulele`` and add a new feature.

- Changes the name of the `pident` column to reflect that it is really the best quality score
- Fixed issues related to errors of "MissingFromTaxDict" (https://github.com/AlexanderLabWHOI/EUKulele/issues/60)
- Allowed gzipped database fastas to be used (https://github.com/nf-core/metatdenovo/issues/256)
- Newest version of EukProt now downloads with `EUKulele` and EukProt protein map bugs have been resolved; gzipped version of fasta also downloads (https://github.com/AlexanderLabWHOI/EUKulele/issues/66)
- Fixed database download issues for GTDB add-on
- Updated calls to `append` with calls to `concat` (`pandas`)
- Fixed some instances of spaces being introduced to taxonomy strings during parsing

New feature:
- Added a flag, `--create_euk_fasta`, to dump a fasta file of eukaryotic sequences after a `EUKulele` run (https://github.com/AlexanderLabWHOI/EUKulele/issues/35)

Adding ability to use GTDB as database selection