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StaG v0.6.0
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@boulund boulund released this 17 Apr 12:46
· 55 commits to master since this release
v0.6.0
ec8a5f9

This StaG release focuses on making the StaG repo conform to modern best practices for Snakemake workflows, and making sure that the KrakenUniq module works with Singularity. It's been approximately four months since the last StaG release (v0.5.1 was released 2022-12-06) and this release contains 60 commits and affects 122 files in the repo. A total of 2474 lines were added and 1118 removed.

Note that due to the new structure of the repo this is a potentially breaking change for some users.

The most notable changes are:

Added

  • Added a new Slurm profile for use on CTMR Gandalf, also intended to be useful
    as a starting point for creating custom Slurm profiles.
  • Added a README with basic instructions for how to configure the workflow.
  • Added function to disable MetaPhlAn heatmap plots, which may be useful when
    processing very large numbers of samples.
  • Added MetaPhlAn-style output tables for KrakenUniq.
  • Added Krona plot output for KrakenUniq.

Fixed

  • Fixed missing interactive Kaiju Krona plots for all samples in final report.
  • Now reusing metaphlan conda environment and biobakery container for running
    bowtie2 mapping rule to ensure a consistent execution environment for bowtie2.
  • KrakenUniq now works in Singularity, thanks to new custom Singularity image.
  • KrakenUniq rule is now correctly not rerun if keep_kraken or keep_kreport
    settings are set to false when executing the workflow a second time.
  • Kraken2 rule is now correctly not rerun if keep_kraken or keep_kreport
    settings are set to false when executing the workflow a second time.

Changed

  • Restructured repo to conform to modern Snakemake best practices. This also
    includes updates to documentation where needed.
  • Hardcoded default thread values for all rules used during local execution
    without profile. Intended to be overridden by profile.
  • Updated KrakenTools to its latest version (1.2), with a minor custom modification
    of kreport2mpa.py, changing output column names to taxon_name and reads.
  • Updated all Python packages in the main stag-mwc conda environment to their
    latest version.
  • Some minor scripts affected by Pandas and Matplotlib updates were modified to
    work with the latest versions of those libraries.
  • Updated groot to 1.1.2 that brings many performance improvements, but removed
    the built-in plotting functionality so the groot module no longer produces
    any plots. Removed size window filtering with BBMap from groot alignment rule,
    and renamed the groot config variable index to index_dir to better map to
    --indexDir used in groot CLI.

Deprecated

  • Older Slurm profiles for CTMR Gandalf and UPPMAX Rackham are now considered
    deprecated and will be removed in a future release.
  • MetaWRAP support is considered deprecated and will eventually be replaced by
    another solution for metagenome assembly in a future release of StaG.
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