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StaG v0.5.1
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@boulund boulund released this 06 Dec 13:43
· 118 commits to master since this release
v0.5.1
207f42a

This StaG release focuses on including recent developments to MetaPhlAn (version 4) and HUMAnN (version 3.6). It's been almost a year since the last StaG release (v0.5.0 was released 2021-11-18) and this release marks the 200th pull request to the StaG project and contains almost 70 commits.

Among the most notable new features are:

  • Support for samplesheet as input: allows decoupling sample names from filenames and allows files from several different locations in the local filesystem or remote sources such as HTTP(S) and S3.
  • Updated MetaPhlAn to v4.0.3
  • Updated HUMAnN to v3.6
  • KrakenUniq module
  • Ability to disable Krona plot generation

Added

  • Produce Snakemake report in zip format instead of HTML due to the HTML report being broken in the later versions of Snakemake.
  • Add KrakenUniq as taxonomic profiler as an alternative with lower false positive rate than Kraken2.
  • Added samplesheet as alternative input file selection method, this also enables providing custom sample names that are not based on pattern in input filenames.
  • Samplesheet can be used to specify remote input files from S3 or HTTP/HTTPS sources.
  • Added run_krona setting for taxonomic profilers to make it possible to disable Krona table and plot creation.

Fixed

  • Corrected typo in host_removal rule concerning keep_kreport config flag.
  • Corrected typo in bowtie2 annotation counts output files leading to workflow complaining about missing output files.
  • Removed unintended stdout printouts from various helper scripts and some MetaPhlAn related rules.
  • Removed outdated mentions of MetaPhlAn2 in report.

Changed

  • Replaced CircleCI automatic testing workflow with one implemented with Github actions.
  • Updated MetaPhlAn to version 4.0.3.
  • Updated HUMAnN to version 3.6.
  • Modified area and MetaPhlAn heatmap plotting scripts to better deal with MetaPhlAn 4 output formats.
  • Updated the documentation to reflect recent changes in StaG.
  • Updated KrakenTools to v1.2
  • Updated scripts/join_tables.py to v1.1, which includes support for skipping lines before the header.
  • Improved automatic report generation code in main Snakefile to be more robust. Now works well also when --use-singularity or --jobs are used simultaneously with --report.

Removed

  • Removed old unmaintained DB download rules for groot, kaiju, kraken2.

Known issues

  • KrakenUniq currently doesn't work with Singularity. Recommended workaround is to run KrakenUniq with --use-conda until it is fixed upstream.
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