Changelog
0.2.2 (2024-11-13)
Bug Fixes
0.2.1 (2024-07-01)
Bug Fixes
0.2.0 (2024-06-28)
Features
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
385 cbioportal export wrapper missing information (#411) (0ac31e8)
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)
added vep to the somatic variant annotation tools (#384) (35cbe09)
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)
feature-complete end-to-end run of the Becnel dataset on hs37d5 & GRCh38.d1.vd1 (#460) (4874074)
implement ngs_mapping fingerprinting (#283) (#289) (a3303ac)
Initial implementation of Molecular bar codes handling using AGeNT (#462) (768dded)
make germline variants pon optional for mutect2 (#375) (30bc591)
make ngs_mapping sub steps generate links (#291) (#294) (6f2edd7)
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)
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)
replacing custom coverage QC scripts with “alfred qc” (#481) (#482) (ae8fe98)
support for snakemake –batch, pipeline.sh for array jobs (#325) (#326) (6ffa5cc)
support for somatic variant calling without normal (#503) (66f555c)
switch GATK 3 HC/UG to GNU parallel based multithreading (#301) (#302) (e23e300)
upgrade to GATK v4.3.0 for gCNV variant calling (#218) (#265) (372464e)
use filtered variants in tmb and signatures (#470) (3e3cead)
Bug Fixes
355 wgs svcnv export external are also affected by changes in the wrapper for varfish annotator (#356) (a660bda)
Add bwa to mbcs meta-tool environment, closes #518 (b3305c5)
add missing mask_duplicates to bwa_mem2 wrapper (#324) (c5cc7a0)
adjustment of manta wrapper for sv_calling_wgs (#351) (e2cd197)
allow to pass single batch number to pipeline_job.sh (#327) (#333) (1c09320)
Always include alfred qc files in input for varfish export bam QC #511 (#516) (d13e595)
bump mehari to 0.21.1 fixes effect prediction (#474) (c0ba296)
bump mehari to v0.25.5 for bugs fixed there (#510) (95b451b)
computation of MD5 sums in gatk4_hc genotype wrapper (#338) (0900d9d)
conda env for merge_multikit_families - install attrs package over attr (#487) (fab3e36)
correct name of annotate_svs in Snakefiles (#344) (#345) (f1355ae)
definition of gcnv conda enviroment for mamba>=1.3 (#452) (#454) (50d0781)
do not expect md5 sums for make_vcf step of melt (#323) (65b45bd)
eb_filter wrapper assuming ANN/CSQ is present (#506) (4dc4948)
enforce ploidy in GATK gCNV ploidy calling wrapper (#377) (f244691)
explicitely enable conda when mamba is disabled (#343) (20bb62c)
explicitly require gawk in mutect2/filter wrapper environment (#498) (6993233)
fixes multiple issues with the recent cbioportal export changes (#425) (740dda5)
fixing gatk4_hc combine_gvcfs wrapper (e489d93)
gcnv contig wrapper scripts do not clean their output folders (#443) (#468) (618f10d)
gcnv wrapper regex curly-brackets parsed by python string formatting (#489 ) (#501) (8fb40e5)
get_output_files from ngs_mapping as reused in variant_export_external (#346) (f4fcd7e)
integration of gcnv and melt into sv_calling_wgs (#350) (5ecad1a)
make GNU parallel more robust with –plain and –workdir (#328) (#331) (5a4c39b)
making compatible with varfish export and mehari (#420) (a40a42d)
mehari wrapper vcf preprocessing does not actually fix info svlen header (#450) (#451) (55146c7)
missing check for
has_annotation
in somatic_variant_filtration rules (#505) (d7420f7)output pattern problem in gatk4_hc/genotyper wrapper (#329) (3d9555d)
pin dependency version in all wrapper conda env yamls (#492) (79499d9)
remove hard coded contig names from gcnv wrappers (#489 ) (#490) (4b89594)
remove some incorrectly expected MELT output (1e24712)
sleep a random time to work around GNU parallel bug (#328) (#337) (de9f2df)
solve issues with variant_export_external and re-enable wgs_cnv_export_external (#354) (47d9e33)
various fixes to make gCNV work properly for WGS and targeted (#370) (14d86e3)
write out pedigrees was missing for sv_calling_wgs (#379) (573c72f)
Reverts
Documentation
Code Refactoring
merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) (#315) (fa7d0e1)
move “bcftools roh” as report in variant_calling (#310) (#311) (ee7e1fa)
rename helper_gcnv_model_target_seq to helper_gcnv_targeted (#303) (#304) (3f36328)
rename targeted_seq_cnv_calling to sv_calling_targeted (#305) (#306) (e234160)