v0.1.1

Maintenance release to make installation run a bit more smoothly.

v0.2.1

0.2.1 (2024-07-01)

Bug Fixes

• switch from setup.py to pyproject toml (#526) (91b1e38)

v0.2.0

0.2.0 (2024-06-28)

Features

• use pydantic models for validation (#496) (bf39678)

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 ([...