Releases: bihealth/snappy-pipeline
Releases · bihealth/snappy-pipeline
v0.3.0
What's Changed
- feat: enabled mbcs meta-tool in the ngs_mapping step model by @ericblanc20 in #545
- feat: Update GCNV environment to 0.9 kernel and GATK4.6.1 by @Nicolai-vKuegelgen in #557
- fix: extra args check by @tedil in #551
- fix: replace vep/run wrapper environment.yaml with symlink to vep environment.yaml by @tedil in #555
- chore: add .readthedocs.yaml for rtd v2 by @tedil in #549
- chore: don't assume mamba is available in tests by @tedil in #552
- chore: Create dependabot.yml by @tedil in #559
- chore: Update dependency constraints by @tedil in #566
- chore: use pydantic short version in tests by @tedil in #569
- chore: fix dependency version constraints by @tedil in #570
Full Changelog: v0.2.2...v0.3.0
Contributors
tedil, Nicolai-vKuegelgen, and ericblanc20
Assets 2
v0.2.2
v0.1.1
v0.2.1
v0.2.0
v0.1.0
0.1.0 (2024-06-28)
⚠ BREAKING CHANGES
- pin dependency version in all wrapper conda env yamls (#492)
- broken plot generation for the control_freec tool in the somatic_wgs_cnv_calling step, and the sample selection for the mutect2 panel_of_normal generation can be based on a user-generated file.
- use snakemake tmpdir resource (#319) (#320)
- merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) (#315)
- merge {variant,wgs_{sv,cnv}}_calling_export into varfish_export (#308) (#309)
- move "bcftools roh" as report in variant_calling (#310) (#311)
- rename targeted_seq_cnv_calling to sv_calling_targeted (#305) (#306)
- rename helper_gcnv_model_target_seq to helper_gcnv_targeted (#303) (#304)
Features
- (430) picard metrics for bam files (#431) (35b24cd)
- 237 revive cnvkit (#339) (bc4c55b)
- 385 cbioportal export wrapper missing information (#411) (0ac31e8)
- 438 vep annotation order (#441) (c28d67e)
- add CI for a scaled down version of a cancer WES pipeline (#499) (b971088)
- add delly2 and manta for sv_calling_targeted (#277) (#307) (99dae5f)
- add missense TMB calculation (#432) (4fd0c73)
- Added support for scarHRD (#429) (c5f9dde)
- added vep to the somatic variant annotation tools (#384) (35cbe09)
- adding bwa_mem2 wrapper (#279) (#312) (1374418)
- Adding tmb calculation (#403) (706a9f5)
- allow helper_gcnv_model_target_seq to build for multiple kits at the same time (#285) (#293) (efe6539)
- also write out mapping quality bigWig file (#476) (#480) (dc1d92b)
- annotating SV coverage with varfish-annotator (#371) (e9fb880)
- bringing back variant_annotation with VEP (#386) (#387) (d4ac11e)
- bump and fix Mehari for SVs in varfish_export (#444) (0ca23f6)
- bump ngs-chew to 0.6.x, adding aafs to output (#317) (feb13a3)
- bump ngs-chew to 0.7 (#334) (7f1fa1a)
- bump ngs-chew to v0.9.x (#478) (c54bba1)
- bump varfish-annotator to v0.32 (#365) (3239564)
- bump varfish-annotator-cli to v0.30 (#314) (#336) (3d045e6)
- change varfish-annotator to mehari (#392) (#393) (c86c665)
- feature-complete end-to-end run of the Becnel dataset on hs37d5 & GRCh38.d1.vd1 (#460) (4874074)
- Fixing Mantis (#427) (e008e7e)
- implement ngs_mapping fingerprinting (#283) (#289) (a3303ac)
- Initial implementation of Molecular bar codes handling using AGeNT (#462) (768dded)
- integrate GATK4 HaplotypeCaller (#287) (#299) (2aeaa01)
- make germline variants pon optional for mutect2 (#375) (30bc591)
- make ngs_mapping sub steps generate links (#291) (#294) (6f2edd7)
- melt for sv_calling_targeted (#321) (13ee84b)
- merge {variant,wgs_{sv,cnv}}_calling_export into varfish_export (#308) (#309) (7c35ec3)
- merge gCNV output in case of multi-kit families (#292) (#465) (ee64a98)
- ngs_mapping cleanup, versions bump (#278) (#280) (af8e21f)
- parallel execution in gatk4_hc_gvcf combine_gvcfs and genotype (#318) (4e888e0)
- path_exon_bed can be provided independent of data type (#389) (#390) (7759d4d)
- PureCN implementation (#453) (e394e8c)
- remove legacy variant callers (#295) (#297) (fa2fc6c)
- remove plot-bamstats ([...