Taxpasta

Fixed

- Repaired the logic for adding taxonomic information to the output table (139).

Added

- Added an option `--ignore-errors` to the `taxpasta merge` command. This allows
ignoring individual profiles that cause errors, like empty profiles (136).

Changed

- Created a special error message for empty profiles, making the cause of the error
much clearer (136).
- Internal restructuring of input validation and transformation services (136).

Added

- Added classifier support for KMCP profiles (129).
- Added a command-line option `--add-rank-lineage` to the `standardise` and
`merge` commands, which inserts a new column `rank_lineage` to results that
contains semi-colon-separated strings with the ranks (130).
- Added a taxonomy table to the BIOM output format when the `--taxonomy` option is
used (134).

Changed

- Reversed the order of lineages printed to output files (131).

Fixed

- Forced reading the `duplicates` and `coverage` columns of KrakenUniq profiles as
float (123).

Added

- Provided curl commands in the intro to quickly fetch example files to try out (97).
- Added new tutorial on merging across classifiers, and warnings why taxpasta
does not currently do this natively (98).
- Added classifier support for ganon report files (109).

Changed

- Made profile validation stricter, such that providing an input from another
than the chosen profiler will usually result in an error (101). The only
exception is that Kraken2 standard profiles can be provided to the
Centrifuge reader, and vice versa, since they are identical in format.

Fixed

- Fixed a few broken internal links (89).
- Simplified getting started tutorial and moved original to complex tutorial (95).
- Improved help text for `--output-format` option to clearly state that it disables
any automatic detection of the output file format (96).
- Extended the MetaPhlAn profile reader to support version 3 & 4 profiles (107).

Added

- Inserted columns with taxonomic information like the name, rank, or lineage of a
taxon at the beginning of the table rather than the end (86).

Fixed

- Enabled handling of MetaPhlAn profiles with taxonomy identifier -1 and combined all
unclassified entries into one with ID 0 (85).
- Generally increased the tolerance in the compositionality checks. Up to 1%
deviation are now allowed; 2% for Bracken profiles (84).