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CHANGELOG.md

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v0.7 changelog

  • 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 changelog

  • 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 changelog

  • 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 changelog

  • 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 changelog

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