- Json report including in stdout upon successful completion (can be disabled with --no-json)
- Renamed
- Support for paired-end files
- Major under the hood changes to use Noodles for fastq parsing, and Niffler to handle compression (RIP my own code)
- Output a fasta file with
--output-fasta - Streamline arguments related to compression types/level
- Improved logging
- Code optimisations
- Increased verbosity of outputs to user
--no-compressflag to output a standard, plaintext fastq file--excludeto exclude specified reads. Works with--childrenand--parents- Docstrings under the hood
- Fixes to reduce memory usage
- Detect and handle
gzfiles or plain files --compressionarg to select compression typezlib-ngto speed up gzip handling--childrenand--parentsto save children and parents based on kraken report
- First release