Gunc

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Features
^^^^^^^^
- GUNC will now report the number of failed genomes if some fail when running in batch mode.

Bugfixes
^^^^^^^^
- Fixed cases where number of mapped genes might be different when running smaller genomes individually vs grouped.
- Fixed cases where gunc would fail if _-_ was in a sequence identifier.
- Fixed cases where contig colour in visualisation was incorrect.
- Fixed incorrect ordering of taxonomic levels in plot if user supplies them in an incorrect order.
- Allow GUNC to continue if some genomes fail diamond mapping.
- Fixed crash if diamond fails to map anything to GUNC reference.
- Fixed bug where GUNC goes into infinite loop if an input filename is merged.fa

Other
^^^^^
- class and order are now included in contig assignment output file (aaronmussig)
- Fix pandas deprecation waring (tmaklin)
- Added fixes for pandas FutureWarning (changing behaviour of Series.idxmax)

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Features
^^^^^^^^
- Added option to plot specific contigs
- Added option to plot ALL contigs

Bugfixes
^^^^^^^^
- Handle cases in which no genes are called with a more useful error message.
- Added check if temp_dir exists before starting analysis.

Other
^^^^^
- Removed dependency on `zgrep` (for compatability with nf-core tests)

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Features
^^^^^^^^
- Added `contig_taxonomy_output` option to output detailed taxonomy assignment count per contig.

Bugfixes
^^^^^^^^
- Fix version of dependancy in conda recipe: requests>=2.22.0

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Bugfixes
^^^^^^^^
- Running with genecalls as iput failed
- GUNC plot contig_display_num displayed a defined number of genes instead of contigs

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Features
^^^^^^^^
- GUNC can now be run with GTDB database
- Added option to download GTDB_GUNC database
- Input file options can be gene_calls (faa) instead of fna if `--gene_calls` flag is set
- Input genecalls can be gzipped
- Output maxCSS file is now sorted


Bugfixes
^^^^^^^^
- Fix version of dependancy: requests>=2.22.0 (older versions not compatable)
- Better error message if gunc_db does not exist
- `checkm_merge` didnt work with unless checkm qa was run with `-o 2`

Other
^^^^^
- Documentation updates
- Links to synthetic datasets added
- Citations for diamond and prodigal added
- Clarified how checkM should be run for `checkm_merge`
- Corrected command for `download_db`
- Check if fasta is given with `-f` option instead of list of filepaths

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Bugfixes
^^^^^^^^
- Running from genecounts failed
- Fixed case where pass.GUNC output was converted to ints
- Fixed silently ignoring input samples that did not map to reference

Other
^^^^^
- Better error message if ouput_dir doesnt exist
- Documentation updates