Hostile

- Allows cross-platform override of the default index cache directory using the environment variable `HOSTILE_CACHE_DIR`. Previously, override using `XDG_DATA_HOME` worked only on Linux. The default continues to be a sensible platform-specific directory determined by the platformdirs library. https://github.com/bede/hostile/issues/32
- Dockerfile simplification (suggested by bdklahn). https://github.com/bede/hostile/issues/33
- Improved usage examples, prompted by ackia. https://github.com/bede/hostile/issues/34

- Automatically download and use any [standard index](https://github.com/bede/hostile#reference-genomes-indexes) by name. This means you can run e.g. `hostile clean --index human-t2t-hla-argos985 --fastq1 reads.fq.gz` and Hostile will fetch that index if it hasn't been downloaded previously. Addresses https://github.com/bede/hostile/issues/28
- Two new standard indexes:
- `human-t2t-hla.rs-viral-202401_ml-phage-202401` (RefSeq viral & [Millard Lab phage](https://millardlab.org/phage-genomes-jan-2024/))
- `human-t2t-hla.argos-bacteria-985_rs-viral-202401_ml-phage-202401` (ARGOS bacteria, RefSeq viral, & [Millard Lab phage](https://millardlab.org/phage-genomes-jan-2024/))
- Improved masking protocol for custom index creation (`hostile mask`)
- Uses `minimap2` with modified secondary alignment limit and secondary-to-primary score ratio threshold (`-N` and `-p`)
- k-merises target genome(s) into 150mers with a step of 10bp by default prior to alignment. Adds dnaio dependency
- New options for `hostile clean`: `--aligner-args`, `--invert`, and `--offline`
- Verification of downloaded index checksums in [manifest.json](https://github.com/bede/hostile/blob/main/bucket/manifest.json) (https://github.com/bede/hostile/issues/20)
- Adds `version`, `aligner` and `options` fields to log output
- Bugfix: when 0 reads remain after decontamination, the resulting empty fastq.gz files are no longer corrupted (https://github.com/bede/hostile/issues/24).
- Disable potentially surprising fallback to Minimap2 if an error is encountered running Bowtie2
- Symlinked FASTQ paths are followed but no longer resolved
- Links to published article

- Adds `hostile fetch` subcommand for viewing and downloading prebuilt references. Readme updated.
- Hostile now automatically chooses a near-ideal number of alignment threads given available CPU count
- Changes optional `--sort-by-name` argument introduced in `0.3.0` to `--reorder`, providing deterministic read order without necessarily sorting
- On platforms other than MacOS (where native `--reorder` performs poorly), `--reorder` uses Bowtie2's native `--reorder` flag, increasing decontamination speed compared to `0.3.0`.

- Adds option `--aligner-args`, allowing arbitrary alignment parameter passthrough (e.g. `--aligner-args="--ignore-quals"`).
- Adds option `--sort-by-name`, ordering output reads by name. This ensures that output order is deterministic when using Bowtie2 with multiple threads. Bowtie2's `--reorder` flag also provides determinism with less overhead on Linux, but has severe performance implications under MacOS in my testing. You can pass `--reorder` to Bowtie2 using `--aligner-args="--reorder"`).

- Addresses 21, improving performance dramatically with Illumina reads / Bowtie in some circumstances
- Adds a space before `/1` and `/2` when renaming Illumina reads (with `--rename`), for improved compatibility
- Improved logging

Fixes issues 10, 19, 20, 22, 23, 25 and added many new tests