The format is based on Keep a Changelog
and this project adheres to Semantic Versioning.
Initial release of umccr/sash, created with the nf-core template.
- Revert hypermutated flag condition in cancer report (reverts >500k sage variant threshold, gpgr#101, bolt#28) (#44)
- Include MANE Plus Clinical transcript ENST00000579755 for CDKN2A alongside MANE Select ENST00000304494, fixing missing gene entries in the Gene Somatic CNV Calls Table when only the NM_058195.4-specific exon has a copy number loss (
umccr_reference_data = '2--1') (#45)
- Fix broken ToC anchor, absolute local path, duplicate word, and misplaced LINX section in
docs/details.md
- Fix
scwatts/sash → umccr/sash and stale CHORD reference in README.md
- Add
sigrap/ and vcf2maf/ to output directory tree; fix inaccurate germline preparation description in docs/output.md
| Tool |
Old |
New |
| bolt |
0.2.17 |
0.2.18 |
- Comprehensive documentation including architecture decision records (ADR), detailed workflow descriptions, and output specifications
- Pipeline overview diagram and quality control metrics documentation
- Enhanced usage documentation with clearer instructions
- Improved output.md with detailed descriptions of all pipeline outputs
- Updated README with better project structure documentation
- Dragen HRD file facultatif
| Tool |
Old |
New |
| bolt |
0.2.15 |
0.2.17 |
| gpgr |
2.2.0 |
2.2.1 |
- Support for oncoanalyser v2.2.0 data structure
- PAVE MNV filtering to remove variants with MNVTAG annotations (see discussion)
- Reference data updates:
- Updated to hmf_pipeline_resources.38_v2.2.0--3
- Process update:
- eSVee parameter updates
- PAVE parameter updates for v1.8 compatibility
- Updated prepare_input paths for oncoanalyser v2.2.0 structure
- Unused reference data files (gridss_region_blocklist, lilac, orange, sigs_signatures, disease_ontology)
| Tool |
Old |
New |
| eSVee |
1.0.3 |
1.1.2 |
| LINX |
2.0.2 |
2.1 |
| PAVE |
1.7.1 |
1.8 |
| PURPLE |
4.1 |
4.2 |
| bolt |
0.2.14 |
0.2.15 |
| gpgr |
2.1.3 |
2.2.0 |
- Software versions are now in
pipeline_info/software_versions.yml
- SV caller: GRIPSS → eSVee
- SV counts (unmelted & melted)
- CNV counts
- TMB-SV counts
- CopyNumberSegment counts
- SV in Circos plots
- Breakpoints & Breakends tables
- Copy-number variants tables
- Genome-wide somatic CNV segment tracks
- SV Map visualisation
- Cancer-report Structural Variants summary plot:
- SR (Split Read) → SF (Split Fragments)
- PR (Paired-Read) → DF (Discordant Fragments)
- Linx v1.25 → v2.0 (affects all Linx reports/files)
- Purple v4.0.1 → v4.1.0
- MSI calculation relay on SAGE-specific tags #7
- (reverted) Circos have link sizes dependent on the size of SV #6
- Filter PoN SV in cancer report tables #8
- Kataegis module
- CHORD HRD metrics
- MSI load and status from purple
- Metric aliases
SR, PR
- GRIDSS/GRIPSS modules