1.0.0

• Automatically download and use any standard index 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 #28
• Two new standard indexes:
  • human-t2t-hla.rs-viral-202401_ml-phage-202401 (RefSeq viral & Millard Lab phage)
  • human-t2t-hla.argos-bacteria-985_rs-viral-202401_ml-phage-202401 (ARGOS bacteria, RefSeq viral, & Millard Lab phage)
• 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 (#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 (#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