The format is based on Keep a Changelog and this project adheres to Semantic Versioning. Naming based on: Audiologists.
- Modules have been updated to remove conda defaults.
| Dependency | Old version | New version |
|---|---|---|
| sanger-tol/blobtoolkit* | 0.6.0 (Bellsprout) | |
| sanger-tol/curationpretext* | 1.0.0 (UNSC Cradle) | 1.1.0 (UNSC Delphi) |
| GFASTATS | 1.3.6--hdcf5f25_3 | |
| MERQUERY_FK | 1.2 | |
| MINIMAP2_ALIGN | 2.28 | |
| SAMTOOLS_MERGE | 1.20--h50ea8bc_0 | 1.21--h50ea8bc_0 |
| SAMTOOLS_SORT | 1.21--h50ea8bc_0 | 1.21--h50ea8bc_0 |
- Blobtookit version was specified in the wrong location, so defaulted to a development branch "draft_assemblies", this has now been updated to v0.6.0.
- Zenodo DOI has now been added to the repo.
Initial release of sanger-tol/ear, created with the nf-core template. The current pipeline means the MVP for ear.
GFASTATS to generate statistics on the input primary genome. MERQURY_FK to generate kmer graphs and analyses of the primary, haplotype and merged assembly. MAIN_MAPPING which is a small mapping subworkflow, that can work with single and paired reads. BLOBTOOLKIT to generate busco files and blobtoolkit dataset/plots. CURATIONPRETEXT to generate pretext plots and pngs.
| Old parameter | New parameter |
|---|---|
| --mapped | |
| --steps |
| Dependency | Old version | New version |
|---|---|---|
| sanger-tol/blobtoolkit* | 0.6.0 (Bellsprout) | |
| sanger-tol/curationpretext* | 1.0.0 (UNSC Cradle) | |
| GFASTATS | 1.3.6--hdcf5f25_3 | |
| MERQUERY_FK | 1.2 | |
| MINIMAP2_ALIGN | 2.28 | |
| SAMTOOLS_MERGE | 1.20--h50ea8bc_0 | |
| SAMTOOLS_SORT | 1.20--h50ea8bc_0 |
* for pipelines, please check their own CHANGELOG file for a full list of software dependencies.
The pipeline depends on a number of databases which are noted in README and USAGE.