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@erinyoung erinyoung released this 28 Feb 16:49
· 119 commits to main since this release
v4.0.20240214
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Welcome to Grandeur version 4!

We expect this version to break everything. For that we are sorry, but we needed to change some things to make the workflow easier to maintain moving forward.

If you have any questions or notice anything not working, please leave an issue, or message @erinyoung via SLACK, email, or however you normally contact her.

Notable changes:

  1. The params have changed. Please review https://github.com/UPHL-BioNGS/Grandeur/wiki#all-parameters-and-their-default-values for params and their default values.
  2. We now use a similar map to nf-core (notably meta.id instead of sample), which will hopefully make this workflow easier to join to other nextflow workflows.
  3. There is now a check for parameters. If a param is unsupported, the workflow will not run.
  4. params.config_file now copies a config file AND params file for the end user
  5. process labels are more in harmony with those of nf-core. We're hopeful this means that institution config files will also work on this workflow.
  6. The phylogenetic analysis workflow has changed. Most notably, roary has been replaced with panaroo. We also have a file that helps to evaluate the core genomes of inputs. An example file can be found at https://github.com/UPHL-BioNGS/Grandeur/wiki/core-genome-evaluation
  7. The default fastani references have been housed in a container. This was done so this repo would be compatible with a cloud system that we are testing.
  8. Documentation has been updated. Please check out our wiki!
  9. Updated containers and fixed bugs (hopefully)

Contributors

erinyoung
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