The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
[0.10.0] - Hideous Zippleback - [2024-04-16]
- OATK module is added into the ORGANELLES subworkflow
- ORGANELLES subworkflow is now called once in the main workflow and runs MITOHIFI in read and assembly mode along with OATK
- ORGANELLES module is now tested in github CI
- NCBI API secret introduced to run MITOHIFI_FINDMITOREFERENCE module
- hifiasm haplotigs are not purged anymore
- Longranger container version is updated
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.
| Dependency | Old version | New version |
|---|---|---|
| mitohifi | 3.0.0 | 3.1.1 |
| oatk | 1.0 |
NB: Dependency has been added if just the new version information is present.
[0.9.0] - Night Fury - [2023-12-15]
Initial release of sanger-tol/genomeassembly, created with the nf-core template.
- Created with nf-core/tools template v2.8.0.
- Implements the basic genome assembly pipeline used in ToL
- Subworkflow to generate Genomescope model
- Subworkflow to generate a raw genome assembly
- Subworkflow to purge haplotigs from primary
- Subworkflow for polishing with 10X data
- Subworkflow for HiC mapping
- Subworkflow for scaffolding
- Subworkflow to run organelles assembly
- Subworkflow to estimate statistics using gfastats, BUSCO, MerquryFK.
| Old parameter | New parameter |
|---|---|
| --input | |
| --bed_chunks_polishing | |
| --cool_bin | |
| --polishing_on | |
| --hifiasm_hic_on | |
| --organelles_on |
NB: Parameter has been added if just the new parameter information is present.
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.
| Dependency | Old version | New version |
|---|---|---|
| bcftools | 1.17, 1.16 | |
| bed_chunks.sh | 1.0 | |
| bedtools | 2.31.0 | |
| busco | 5.4.3 | |
| bwamem2 | 2.2.1 | |
| coverage.sh | 1.0 | |
| cooler | 0.8.11 | |
| cut | 8.30 | |
| fastk | f18a4e6d2207539f7b84461daebc54530a9559b0 | |
| freebayes | 1.3.6 | |
| gatk4 | 4.4.0.0 | |
| genescope | 380815c420f50171f9234a0fd1ff426b39829b91 | |
| gfastats | 1.3.5 | |
| GNU Awk | 5.1.0 | |
| hifiasm | 0.19.3-r572 | |
| juicer | 1.1 | |
| juicer tools | 1.9.9 | |
| longranger | 2.2.2 | |
| merquryfk | 8ae344092df5dcaf83cfb7f90f662597a9b1fc61 | |
| minimap2 | 2.24-r1122 | |
| mitohifi | 3.0.0 | |
| pigz | 2.3.4 | |
| pretextmap | 0.1.9 | |
| pretextsnapshot | 0.0.4 | |
| purge_dups | 1.2.5 | |
| python | 3.11.0, 3.8.1 | |
| R | 4.2.0 | |
| samtools | 1.17, 1.16.1 | |
| seqtk | 1.3-r106 | |
| yahs | 1.2a.1 | |
| yaml | 6.0 |
NB: Dependency has been added if just the new version information is present.