4.5.24310

Minor release:

• Update mlst to 2.23.0-2024-11-01
• Update blast to 2.16.0
• Update elgato to 1.20.1
• Update iqtree2 to 2.3.6
• Update datasets to 16.30.0
• Update pbptyper to 2.0.0

4.5.24276

Minor release:

Updates mlst to 2.23.0-2024-10-01

4.5.24250

Minor update

• Update amrfinder to 3.12.8-2024-07-22.1
• Update elgato to 1.19.0
• Update mlst to 2.23.0-2024-09-01

4.5.24219

Minor release:

• update mlst to 2.23.0-2024-08-01
• update spades to 4.0.0
• update datasets to 16.22.1

4.5.24184

Minor "update"

• downgrades iqtree2 back to 2.3.1 because of cloudwatch issues

4.5.240626

Moderate Update:

Container Updates:

• updates iqtree2 to 2.3.4
• updates mlst to 2.23.0-2024-06-01
• updates datasets to 16.15.0
• adds Yersinia to the refs that Grandeur uses for Fastani (version 2024-06-26)

Possibly breaking updates:

• removed flag process and replaced with some groovy functions
  Note: works for me!

4.4.240521

Moderate update

• "under the hood" uses some different channels because sometimes spades doesn't fail, but then also doesn't create a consensus fasta file
• updates panaroo to 1.5.0
• updates iqtree2 to 2.3.1
• updates mlst to 2.23.0-2024-05-01
• updates amrfinder to 3.12.8-2024-05-02.2
• updates datasets to 16.15.0

Of note, according to NCBI announcement https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/, blast databases are getting cleaner. I recommend updating any blast databases for efficiency and accuracy.

4.2.20240425

Moderate release:

• Allows user to use roary for multiple sequence alignment with aligner param (param.aligner = 'panaroo' as default)
• Updates AMRFinder container to 3.12.8-2024-01-31.1_2
• Updates datasets to 16.10.3
• Updates mlst to 2.23.0-2024-04-01
• Updates plasmidfinder to 2.1.6_2024-03-07
• Updates Seqsero2 to 1.3.1
• Updates serotypefinder to 2.0.2

4.0.20240312

Minor release, which is mostly some bug fixes and database updates.

Updates

• mlst to 2.23.0-2024-03-11
• amfinderplus to 3.12.8-2024-01-31.1

Fixes

• #180
• #178
• #177
• #176
• #174 (hopefully)

4.0.20240214

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)