Enhancements & fixes
- Runtime of the blast commands is now capped at 12 hours (#166)
- Upgraded Busco and added an option to control the gene predictor used (#160, #174, #181)
- nf-core template upgrade (to version 3.2.1) (#164, #176)
- Documentation fixes (broken links) (#175)
- Ability to run without any read data (#177)
Software dependencies
Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only Docker or Singularity containers are supported, conda is not supported.
| Dependency | Old version | New version |
|---|---|---|
| blobtoolkit | 4.4.4 | 4.4.6 |
| busco | 5.7.1 | 5.8.3 |
Parameters
| Old parameter | New parameter |
|---|---|
| --busco_gene_predictor |
NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.