v3.0

What's Changed

• Update workflow to be compatible with Snakemake v8
• Add NEEAT algorithm to filter out noise
• Add functionality to assign taxonomy to ASVs
• Add preprocessing (length + codon filtering)
• Rename output files
• Add container directives to rules
• Add pixi project file
• Use checkpoints for parallelization

Full Changelog: v2.1...v3.0

Version 2.1

Changelog

• Change chimera default method to "samplewise"
• Change parameters for swarm in default config file
• Use mamba as conda frontend in slurm profile
• Add script to calculate pairwise distances between ASVs in final output
• Add uchime algorithm as configurable to chimera filtering and require perfect
  matches for uchime2_denovo and uchime3_denovo
• Make sure ASV counts are treated as integers when preparing input
• Handle division by zero in calculating precision/recall
• Use pandas apply when calculating representative max count

Version 2.0

Changelog

• Add description about FINBOL benchmark data
• Add chimera detection and filtering rules
• Reorder output structure to better handle different runs of chimera detection/ASV clustering

Version 1.0

First release of ASV-clustering workflow