The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
[1.1.6] - Shang Tang (patch 6) - [2025-02-10]
- Allow DeepVariant and BCFtools to handle CSI files
- Deal with genomes >4GB in Minimap
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 |
|---|---|---|
| nextflow | 22.10.1 | 23.10.1 |
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.
[1.1.5] - Shang Tang (patch 5) - [2025-01-14]
- Fix bug in alignment subworkflow
[1.1.4] - Shang Tang (patch 4) - [2024-12-05]
- Module updates and remove Anaconda references
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 |
|---|---|---|
| bcftools | 1.17 | 1.20 |
| blastn | 2.14.1 | 2.15.0 |
| deepvariant | 1.5.0 | 1.6.1 |
| Python | 3.8.3 | 3.9.1 |
| 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.
[1.1.3] - Shang Tang (patch 3) - [2024-05-24]
- Fixed the bug in the filtering of multiple PacBio files
[1.1.2] - Shang Tang (patch 2) - [2024-03-14]
- Bug fix when index fai file given for reference fasta file
This release with the following initial parameters:
| Old parameter | New parameter |
|---|
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.
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 |
|---|
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.
[1.1.1] - Shang Tang (patch 1) - [2024-02-02]
- Bug fix when reference fasta file name end with .fa or .fa.gz
This release with the following initial parameters:
| Old parameter | New parameter |
|---|
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.
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 |
|---|
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.
[1.1.0] - Shang Tang - [2023-12-20]
- Updated the CI procedure to use "sanger-tol" rather than "nf-core" names.
- Renamed Sanger related Github CI test workflows.
- nf-core template was updated from 2.7 to 2.8.
- Removed BAM/CRAM index files from the sample sheets.
- Made fasta index file optional from the inputs.
- Imported PacBio readmapping sub-workflows from sanger-tol/readmapping pipeline. Therefore, the pipeline can run on unaligned BAM/CRAM samples now.
- Use VCFtools to calculate per site nucleotide diversity.
- Use VCFtools to calculate heterozygosity.
This release with the following initial parameters:
| Old parameter | New parameter |
|---|---|
| --gzi | |
| --vector_db | |
| --align | |
| --include_positions | |
| --exclude_positions |
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.
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 |
|---|---|---|
| DeepVariant | 1.4.0 | 1.5.0 |
| samtools | 1.16.1 | 1.17 |
| bcftools | 1.16.1 | 1.17 |
| python | 3.11.0 | 3.11.4 |
| vcftools | 0.1.16 | |
| blast | 2.14.1+ | |
| gunzip: | 1.10 | |
| minimap2 | 2.24-r1122 | |
| awk | 5.1.0 | |
| untar | 1.30 |
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.
[1.0.0] - Xia Yu - [2023-05-03]
Initial release of sanger-tol/variantcalling, created with the nf-core tools.
- Created with nf-core template v2.7.2.
- Allows calling variants using DeepVariant for PacBio long read data.
- Significant speed improvements made by splitting the genome before calling variants.
- Outputs both vcf and gvcf formats.
This release with the following initial parameters:
| Old parameter | New parameter |
|---|---|
| --input | |
| --fasta | |
| --fai | |
| --gzi | |
| --interval | |
| --split_fasta_cutoff |
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.
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 |
|---|---|---|
| DeepVariant | 1.4.0 | |
| samtools | 1.16.1 | |
| bcftools | 1.16.1 | |
| nextflow | 22.10.6 | |
| python | 3.11.0 | |
| python | 3.8.3 | |
| pigz | 2.3.4 | |
| yaml | 6.0 |
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.