This StaG release is a considered a major release due to the removal of several main workflow sections, specifically all antibiotic resistance gene tools and the assembly workflow have been removed. Users interested in AMR profiling should consider using the BBMap or Bowtie2-based mapping workflows in StaG, or turn to another Snakemake or Nextflow workflow for that type of profiling (e.g. the latest AMR++ release). This StaG release also adds a new feature: host removal using Bowtie2, intended to be used for high-host microbiome samples in combination with Kraken2 because we have found that Kraken2 is very sensitive to remaining host contamination left behind after Kraken2-based host removal. We find that if performing taxonomic profiling with MetaPhlAn4 the quality of host removal has no substantial impact on the quality of the taxonomic profiles and users can benefit from continuing to use Kraken2 for host removal to save some time and compute resources in those cases. In addition, there is a critical bug fix when running HUMAnN3 that all users should upgrade to.
The previous StaG release, v0.6.1 was two weeks ago. The v0.7.0 release modifies approximately 35 files and removes approximately 1472 lines of code, with 381 new lines.
[0.7.0] 2023-06-13
Added
- Host removal: Bowtie2 now available as an option for host removal.
Fixed
- HUMAnN3: Fixed critical bug leading to entire system-wide temporary directory being emptied after successful HUMAnN run.
- Singularity: All Singularity definition files should from now on get version bumps in the description labels when conda environments built inside them are updated to reduce the risk of Singularity reusing old cached copies of images instead of downloading the latest version as intended.
Changed
- Preprocessing summary: Preprocessing summary script can now output a table of read counts regardless of which combination of read QC and host removal is used.
Removed
- AMR++, Groot: All tools for antibiotic resistance gene profiling have been removed entirely because they were out of date and had few active users. Users wanting to perform antibiotic resistance gene profiling are suggested to use the mapper modules with a suitable reference database or run the latest version of AMR++ separately.
- Assembly: The MetaWRAP-based assembly parts of the workflow have been removed entirely.