Gtdbtk

* Updated GitHub CI/CD to trigger docker build / tag version on release.
* (255) (297) Fixed `'Namespace' object has no attribute` errors by adding default arguments to argparse.

* Check if stdout is being piped to a file before adding colour.
* (283) Significantly improved classify performance (noticeable when running trees > 1,000 taxa).
* Automatically cap pplacer CPUs to 64 unless specifying `--pplacer_cpus` to prevent pplacer from hanging.
* (262) Added `--write_single_copy_genes` to the identify command. Writes unaligned single-copy AR122/BAC120 marker genes to disk.
* When running -version warn if GTDB-Tk is not running the most up-to-date version (disable via `GTDBTK_VER_CHECK = False` in config.py). If GTDB-Tk encounters an error it will silently continue (3 second timeout).
* (276) Renamed the column `aa_percent` to `msa_percent` in summary.tsv (produced by classify).
* (286) Fixed a file not found error when the reference data is a symbolic link (thanks davidealbanese!).
* (277) Fixed an issue where if the user overrides the translation table using the optional 3rd column in the batchfile, the other coding density would appear as -100. Both translation table densities are now reported.
* The check_install command now also checks that all third party binaries can be found on the system path.
* The align step is now approximately 10x faster.
* (289) Added `--min_af` to classify and classify_wf which allows the user to specify the minimum alignment fraction for FastANI.
* Added the `--mash_db` command to re-use the GTDB-Tk Mash reference database in ani_rep.

This version of GTDB-Tk requires a new version of the GTDB-Tk reference package (gtdbtk_r95_data.tar.gz) available [here](https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/auxillary_files/gtdbtk_r95_data.tar.gz).

Features:
* Updated reference package to use the GTDB Release 95 taxonomy.
* Report if the species-specific ANI circumscription criteria is satisfied in the ani_closest.tsv file output by ani_rep.
* Estimated time until completion has been dampened.

Bug fixes:
* (241) Moved GTDB-Tk entry point to __main__.py instead of bin/gtdbtk to support execution in some HPC systems (gtdbtk will still be aliased on install).
* (251) Allow parsing of FastANI v1.0 output files. However, a warning will be displayed to update FastANI.
* (254) Fixed an issue where --scratch_dir would fail, and not clean-up the mmap file.

Features:
* (242) Added the decorate command allowing the de novo workflow to be run
* (244) Added the infer_rank method which established the taxonomic ranks of internal nodes of user trees based on RED
* (248) If the identify command is run on the same directory, genomes which were already processed will be skipped.
* (248) Improved pplacer output with running the classify command

- Fix a issue with Tree parsing

* *Bug fixes:*
* In rare cases pplacer would assign an empty taxonomy string which would raise an error.
* ([229](https://github.com/Ecogenomics/GTDBTk/issues/229)) Genomes using windows line carriage `\r\n` would raise an error.
* ([227](https://github.com/Ecogenomics/GTDBTk/issues/227)) CentOS machines would fail when using `~` in paths.
* The bac120 symlink was pointing to the archaeal tree when using the `root` command.
* *Features:*
* Updated the `gtdb_to_ncbi_majority_vote.py` script for translating taxonomy.
* ([195](https://github.com/Ecogenomics/GTDBTk/issues/195)) Added the `--pplacer_cpus` argument to specify the number of pplacer threads when running `classify` and `classify_wf` (#195).
* ([198](https://github.com/Ecogenomics/GTDBTk/issues/198)) The `--debug` flag of `align` outputs aligned markers to disk before trimming.
* ([225](https://github.com/Ecogenomics/GTDBTk/issues/225)) An optional third column in the `--batchfile` will specify an override to which translation table should be used.
Leave blank to automatically determine the translation table (default).
* ([131](https://github.com/Ecogenomics/GTDBTk/issues/131)) Users can now specify genomes which have NCBI accessions, as long as they are not GTDB-Tk
representatives (a warning will be raised).
* ([191](https://github.com/Ecogenomics/GTDBTk/issues/191)) Added a new command `ani_rep` which calculates the ANI of input genomes to all GTDB
representative genomes.
* This command uses [Mash](https://github.com/marbl/Mash) in a pre-filtering step. If pre-filtering is enabled (default)
then `mash` will need to be on the system path. To disable pre-filtering use the `--no_mash` flag.
* ([230](https://github.com/Ecogenomics/GTDBTk/issues/235)) Improved how markers are used in determining the correct domain, and gene selection for the alignment.