v0.9-alpha

v0.9 changelog

• Refactored codes, split sections into modules
• Added GreenGenes 2024.10, updated GTDB to r220, and Silva to 138.2, please rerun download_db to get the latest version
• Added new parameter --db_to_prioritize to allow users to specify which database to prioritize for taxonomy assignment.
  • Prioritization of assignment by default is now GG2, then GTDB, then Silva.
• Attempt to make tmpdir and cachedir more robust for QIIME2-related processes
  • TMPDIR is now set to the current working directory
• Update QIIME2 to 2024.10 version. Workflow tested with Nextflow 24.11.0
• Switched to using QIIME2 official container instead of self-built one.

v0.7

Minor release mainly to update Qiime2 version.

• New feature to limit reads to N reads (--downsample) in case of samples with extremely high depth.
• Updated Qiime2 to 2023.2 version (This should not affect downstream results) to get rid of annoying installation issue with old Qiime2 version.

v0.5

• Allow splitting samples into group for dada2 noise (pool column in metadata TSV, see
  GitHub documentation here).
• #22: Added --publish_dir_mode to allow users to specify if they want the outputs in
  other modes such as hardcopy instead of the default Nextflow behaviour (absolute symlinks).
• Handle a minor bug in visualize_biom.Rmd script whereby if the samples are extremely
  similar to each other, MDS plotting will fail.
• Cleaned up code with small changes to allow pipeline to run on AWS. Big thanks to
  collaborator from AGRF Australia for initiating, testing and providing feedbacks.

v0.4

• Fix some bugs wrongly displaying Naive-Bayes statistics as VSEARCH stats in HTML
• Allow manually specifying primers with --forward_p and --adapter_p for
  cutadapt
• Allow skipping Naive-Bayes classification via the --skip_nb parameter. This
  allows user to easily use any database with VSEARCH and generate report. See FAQ.
• Fixed bug preventing single sample heatmap from displaying
• Save versions and parameters in parameters.txt for reproducibility
• Updated QIIME 2 environment YAML.
• Fixed issue 17 reported by Stephane. Nextflow and Mamba do not need to be installed
  at base conda environment.

v0.3

• Updated naive classifier approach to use GTDB r207 (updated from r202) and make GTDB r207 the first priority so it's more consistent with VSEARCH-based classification. I.e. in the naive classification approach, ASVs are classified firstly by GTDB before Silva and RefSeq (In v0.2, Silva was the first priority).
• New feature: Optional PICRUSt2 for pathway inference.
• Databases are now downloaded from a central Zenodo DOI to make process more robust: https://zenodo.org/record/6912512

v0.2

Starts tracking version, no main changes compared to previous version except that the pipeline is now versioned.