All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
### Changed
- Updated documentation
- Reconciled workflow with wf-template v5.2.6
- Updated aplanat to v0.6.20
- Updated documentation
- Memory requirements for each process
- Updated whole workflow to bring up-to-date with recent template changes
- Configuration for running demo data in AWS
- Updated sample sheet to expect a file
- Updated description in manifest
- Documentation
- Nextflow schema
- Report card more intelligent to drop-outs
- Group 2 SNPs now included in reports
- CSV is more straight forward to interpret
- Single sample report uses results from previous reporting step
- Appendix report removed
- Group 3 variants no longer reported
- VariantDB - added ONT reviewed variants
- Added coverage details to CSV
- Warning to single sample report in the case of target failure
- ONT reviewed group 3 variants are now reported (moved to V3)
- No reads in NTC causing whatshap failure
- Annotation issue for MNPs
- Phasing issue where variant at pos 1 & 3 but not 2
- Base image to v0.2.0
- Issue with phased variants
- Issue with report when there are unclassified reads
- Fastqingress metadata map
- Group 2 and group 3 variants to csv
- EMB M306I - now ignoring strand bias filter
- Issue with changes to ingress and reports
- Better help text on cli
- Adding variants to csv output
- Keep only mapped reads
- Downgraded pomoxis to prevent issues with empty bams
- Wording on reports
- bcftools mpileup now uses bed file to speed up processing
filetopathin nextflow process definitions
- Issue where Rv0678 was excluded from variant DB
- Crude downsampling step to expedite high coverage samples
- Error in phred strand bias calc if p=0
- Unclassified reads caused failure due to lack of barcode
- CSV output of final results for every sample
- Fixed issue with resistance calling
- Some wording on reports
- Removed "_blank" from single sample reports for jupyter compatibility
- Report formatting
- New docs format
- Major restructuring to use bcftools mpileup
- Phasing with whatshap
- VCF files used throughout
- Unit tests
- Parsing of WHO catalogue xlsx file
- Tidying up of reference files
- Added option to set strand bias filter level
- Added versions for primers
- Sample name given by user can now be an integer
- Single sample reports
- Additional report on less confident variants
- Update to primers
- Typos
- Schema consistency
- Bumping aplanat to >=v0.6.1 for bootstrap 4
- Schema issues with labslauncher
- Improved report
- Some rationalisation of ancillary files
- Schema changes for labslauncher
- Fastq ingress reverted & unclassified ignored in
main.nf
- New code to genotype variants with pileup
- No medaka or nanopolish steps
- Updates to schemas to bring in line with other workflows
- Thresholds for negative and positive controls
- Fastqingress module for common handling of (possibly multiplexed) inputs.
- Optimized container size through removal of various conda cruft.
- Use mamba by default for building conda environments.
- Cut down README to items specific to workflow.
- Incorrect specification of conda environment file in Nextflow config.
- Explicitely install into base conda env
- Software versioning report example.
- Version bump to test CI.
- Moved all CI to templates.
- Use canned aplanat report components.
- CI release checks.
- Create pre-releases in CI from dev branch.
First release.