Tourmaline V2 beta

What's Changed

Tourmaline V2 is now the default version!

Major changes

• Run via tourmaline.sh script
• Ability to provide externally-generated data
• Three steps, three config files: qaqc, repseqs, taxonomy
  • Sequence quality assurance and quality control (qaqc)
  • Denoising and ASV generation (repseqs)
  • Taxonomy assignment (taxonomy)
• format_analysisMetadata.py script to generate bioinformatics metadata in FAIRe format
• readthedocs documentation site: https://tourmalinedocs.readthedocs.io

New Contributors

• @clementcoclet made their first contribution in #173

Full Changelog: v1.1.1...v2.0.0-beta

qiime2-2023.5 version

What's Changed

Updated Tourmaline to work with qiime2-2023.5. In this version, you must install snakemake in a separate environment, and run Tourmaline commands in the snakemake environment.

Breaking changes

• Qiime2 artifacts created with qiime2-2023.5 are NOT backward compatible with previous versions of qiime2 or Tourmaline. Artifact created with previous versions are compatible with this version, though.

Feature updates

• Added export_asv_taxa_obis rule to create 01-taxonomy/asv_taxa_sample_table.tsv file that combines ASV sequences, taxonomy, and per-sample read counts. This file can be used for conversion to OBIS/GBIF format.
• Added support for user-provided classifier when doing naives-bayes. Must be provided as "classifier.qza" in the "01-imported/" folder.

qiime2-2023.2 version (v1.0.1)

Updates to documentation for qiime2-2023.2 version, including creation of a wiki folder for storing Wiki markdown files.

qiime2-2023.2 version

What's Changed

• Update Tourmaline Snakemake and config.yaml files to work with Qiime2-2023.2
• Update installation instructions
• New snakemake rule to filter out samples by name or metadata
• Uses newest Muscle v5
• records database version in config file

New Contributors

• @cuttlefishh made their first contribution in #1
• @lukenoaa made their first contribution in #17
• @ksilnoaa made their first contribution in #83
• @7yl4r made their first contribution in #81

Full Changelog: https://github.com/aomlomics/tourmaline/commits/v1.0.0