Release v2.2.0

What's Changed

• annotate blast results speedup (9f831c4)
• removing uv python bytecode issue (99aaae9)
• fixing formatting for some of the python scripts we've been modifying (b3086b0)
• part 2: ensure process inputs track validation (79ba788)
• split calidation into two processes (17ff37b)
• bug fix: pairing read counts with blast results by sampleId (08d94f9)
• fixing blastn and megablast results not uploading (55d9b4a)
• removing filtering from the lca annotation script for better separation of concerns (9d89cfa)
• fixing a bug in supplying flags to samtools view (630ff66)
• formatting fix (afa1bec)
• megablast hit filtering fix and minor logging changes (6d858de)
• making spades optional and handling polars schema overrides earlier (dc205a1)
• bug fix: blast task validation naming discrepency (632aa78)
• maxing out resources for spades and fixing a bug where labkey bundling processes were given a nonexistent label (75591e2)
• fixing how blast results are interpreted by the parser instead of delegating to lazy casts in the polars hit selection script (58d092b)

Contributors

Thanks to: Nicholas Minor,wkgardner

Version Information

• Version: 2.2.0
• Tag: v2.2.0
• Commit: 9f831c4

Installation

Using this release with Nextflow:

nextflow run dhoconno/nvd -r v2.2.0 \
    --tools all \
    --samplesheet your_samples.csv \
    --experiment_id your_experiment_id \
    [other parameters...]

Development setup:

git clone --branch v2.2.0 https://github.com/dhoconno/nvd.git
cd nvd
pixi install --frozen
pixi shell

Documentation

• Example Commands
• Contributor Guide
• Main README