BALSAMIC v11.0.0 release

ivadym commented 2 years ago

Balsamic features for the next release:

Balsamic v11/v12 discussion

[ ] Filtering strategy prior to upload to Scout

[ ] ENCODE Blacklist regions

[ ] Merge TNhaplotyper and TNscope before annotation for T-only analysis.

[ ] Post-annotation filtering

[ ] Database of somatic and germline variants using DNAscope VCF?

[ ] Ranking to order variants

Annotation

[x] loqusdb CLI for WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/992
[x] loqusdb normal SNV Frequencies for WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1012
[x] loqusdb normal SV Frequencies for WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1013
[x] Swegen SV and SNV Frequencies for WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1014
[x] Update documentation

Filtering strategy prior to upload to Scout

[x] Add Pre-annotation filtering, WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1013
[x] Add research and clincal VCFs, WGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1007
[x] Add Pre-annotation filtering, research and clinical VCF TGA: https://github.com/Clinical-Genomics/BALSAMIC/pull/1024
[x] CG: https://github.com/Clinical-Genomics/cg/issues/1559
[x] Split vep germline rules: https://github.com/Clinical-Genomics/BALSAMIC/pull/1018
[x] Implement filtering against loqusdb observations: https://github.com/Clinical-Genomics/BALSAMIC/pull/1029
[x] Implement filtering against swegen SV and SNV: https://github.com/Clinical-Genomics/BALSAMIC/pull/1029
[x] Update documentation

Rescue filtered out variants:

[x] #986 https://github.com/Clinical-Genomics/BALSAMIC/pull/1021
[x] #975 https://github.com/Clinical-Genomics/BALSAMIC/pull/1021
[x] Update documentation

Variant callers

[x] Add CNVpytor for WGS T-only analysis: https://github.com/Clinical-Genomics/BALSAMIC/pull/994
[ ] Add CNVpytor for WGS T-N analysis
[x] Disable TNhaplotyper for WGS tumor-normal: https://github.com/Clinical-Genomics/BALSAMIC/pull/988
[x] Disable TNhaplotyper for WGS tumor-only: https://github.com/Clinical-Genomics/BALSAMIC/pull/1006
[x] Disable TNhaplotyper for TGS: https://github.com/Clinical-Genomics/BALSAMIC/pull/1022
[x] Update documentation

PON

[x] Generate a panel of normal reference and use it as input for BALSAMIC analysis
- [x] Balsamic CLI, https://github.com/Clinical-Genomics/BALSAMIC/pull/983
- [x] CGbalsamic-pon workflow & automatic fetching of a PON file for targeted analysis if available, https://github.com/Clinical-Genomics/cg/pull/1533
- [x] Update documentation, https://github.com/Clinical-Genomics/atlas/pull/868

Scout

[x] Add CNVpytor PDF to Scout https://github.com/Clinical-Genomics/BALSAMIC/pull/1023

Update delivery report

[x] Delivery report generated and delivered to Caesar, https://github.com/Clinical-Genomics/cg/pull/1536
[x] Delivery report to contain VCF file names that were used in analysis and uploaded to Scout, https://github.com/Clinical-Genomics/cg/pull/1536
[x] Show version information regarding tools used in analysis (extracted from the config.json file), https://github.com/Clinical-Genomics/cg/pull/1536
[ ] Delivery report for QC only analysis
[x] Update documentation

File delivery

[x] Update stored and delivered files (HERMES & CG)
[x] Update documentation
[ ] Update atlas

Feature Update

[ ] Version information regarding tools and databases used in analysis
[x] Update cluster.json for cpu and time
[ ] Add memory in cluster.json
[x] Add cluster configuration for processes missing them and for the newly added processes: https://github.com/Clinical-Genomics/BALSAMIC/pull/1028
[ ] Move fastq concatenation from CG to BALSAMIC (https://github.com/Clinical-Genomics/BALSAMIC/issues/993):
- [ ] Remove concatenation for BALSAMIC in CG
- [ ] Adapt the CLI to accept multiple reads and concatenate the fastqs

Bug Fixes

[x] invalid flag for mate and cluster resources https://github.com/Clinical-Genomics/BALSAMIC/pull/1025/files
[x] shell condition & remove tnhaplotyper https://github.com/Clinical-Genomics/BALSAMIC/pull/1022
[x] sam validation error https://github.com/Clinical-Genomics/BALSAMIC/pull/1019, https://github.com/Clinical-Genomics/BALSAMIC/pull/1027
[x] cnvkit container and add input VCF file https://github.com/Clinical-Genomics/BALSAMIC/pull/995/files
[x] cnvkit container https://github.com/Clinical-Genomics/BALSAMIC/pull/996/files
[x] add missing R pachages to cnvkit container https://github.com/Clinical-Genomics/BALSAMIC/pull/997
[x] rlang for cnvkit conatainer https://github.com/Clinical-Genomics/BALSAMIC/pull/998
[x] Increase sambamba run time https://github.com/Clinical-Genomics/BALSAMIC/pull/1001
[x] python packages causing test_workflow to fail https://github.com/Clinical-Genomics/BALSAMIC/pull/1008
[x] sam validation error https://github.com/Clinical-Genomics/BALSAMIC/pull/1019
[x] invalid flag for mate and update commands https://github.com/Clinical-Genomics/BALSAMIC/pull/1025
[x] fixes cli documentation in the balsamic readthedocs https://github.com/Clinical-Genomics/BALSAMIC/pull/979

Timeline:

To be defined (Nov).

vwirta commented 2 years ago

Discussion: move fastq concatenation from cg (on log-in node) to balsamic (enables use of slurm on hasta) @ivadym @henrikstranneheim @moahaegglund

ivadym commented 1 year ago

Deployed in production.

Not addressed point has been moved to https://github.com/Clinical-Genomics/BALSAMIC/issues/1048

Clinical-Genomics / BALSAMIC

BALSAMIC v11.0.0 release #989