Enhancements & fixes
- New annotation_statistics subworkfow which runs BUSCO in protein mode and generates some basic statistics on the the annotated gene set if provided with a GFF3 file of gene annotations using the
--annotation_setoption. - The genome_metadata subworkflow now queries Ensembl's GraphQL API to determine if Ensembl has released gene annotation for the assembly being processed.
- Module updates and remove Anaconda channels
- Removed merquryfk completeness metric
Parameters
| Old parameter | New parameter |
|---|---|
| --annotation_set |
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.
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 |
|---|---|---|
agat |
1.4.0 | |
bedtools |
2.30.0 | 2.31.1 |
busco |
5.5.0 | 5.7.1 |
cooler |
0.8.11 | 0.9.2 |
fastk |
427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c | 666652151335353eef2fcd58880bcef5bc2928e1 |
gffread |
0.12.7 | |
merquryfk |
d00d98157618f4e8d1a9190026b19b471055b22e | |
multiqc |
1.14 | 1.25.1 |
samtools |
1.17 | 1.21 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.