Releases v0.1.0
tedil
released this
28 Jun 15:07
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
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 )
adjust STAR to new ngs_mapping (#366 ) (#367 ) (65c5b6e )
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 )
bump melt memory further (#374 ) (fad1ad6 )
bump time of ngs_mapping/bam_collect_doc (#394 ) (04551d5 )
bwa_mem2 wrapper only used right read (#316 ) (53c88aa )
check whether gCNV is enabled correctly (#357 ) (e5ec1b3 )
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 )
fix somatic snappy (#477 ) (#491 ) (af961cc )
fix trimadap-mt & bbduk java version (#446 ) (46b2303 )
fixes multiple issues with the recent cbioportal export changes (#425 ) (740dda5 )
Fixing feature-effects compression (#440 ) (98825db )
fixing gatk4_hc combine_gvcfs wrapper (e489d93 )
fixing problem in running varfish-export (#378 ) (6d95d88 )
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 )
give Delly more memory (#373 ) (05f7988 )
give melt more memory (#372 ) (33785b2 )
icrease allowed running time of gCNV jobs (#349 ) (78521f5 )
integration of gcnv and melt into sv_calling_wgs (#350 ) (5ecad1a )
interpret skip_libraries in sv_calling (#383 ) (60be51d )
make GNU parallel more robust with --plain and --workdir (#328 ) (#331 ) (5a4c39b )
making compatible with varfish export and mehari (#420 ) (a40a42d )
manta germline_targeted wrapper (#361 ) (8e718c2 )
mehari wrapper vcf preprocessing does not actually fix info svlen header (#450 ) (#451 ) (55146c7 )
melt wrappers (#335 ) (66fcd46 )
missing check for has_annotation in somatic_variant_filtration rules (#505 ) (d7420f7 )
output pattern problem in gatk4_hc/genotyper wrapper (#329 ) (3d9555d )
paths in gcnv wrappers (#380 ) (fcece11 )
pin dependency joblib of gcnv (#412 ) (02fa2da )
pin dependency version in all wrapper conda env yamls (#492 ) (79499d9 )
popdel wrappers (#362 ) (07d73f4 )
re-enabling and fixing Popdel (#359 ) (b28ed75 )
remove "tar results" from manta wrappers (#376 ) (9717be7 )
remove hard coded contig names from gcnv wrappers (#489 ) (#490 ) (4b89594 )
remove some incorrectly expected MELT output (1e24712 )
rename _version.py to version.py (#521 ) (4fb8d8d )
set locale to C in bcftools/TMB wrapper (#507 ) (9789a2d )
setup.py had reference to removed script (#330 ) (30447bd )
sleep a random time to work around GNU parallel bug (#328 ) (#337 ) (de9f2df )
sleep syntax in Manta wrappers (#358 ) (e50d4d4 )
solve issues with variant_export_external and re-enable wgs_cnv_export_external (#354 ) (47d9e33 )
update snakemake version requirements (#398 ) (427803c )
use local /tmp directory in gcnv wrapper (#363 ) (cf052c7 )
use only one thread for MELT (#322 ) (ee84aa4 )
various fixes to make gCNV work properly for WGS and targeted (#370 ) (14d86e3 )
write out pedigrees was missing for sv_calling_wgs (#379 ) (573c72f )
zcat usage in bwa_mem2 wrapper (#364 ) (9cc0bb2 )
Reverts
Documentation
add warning for writing new workflow steps (#400 ) (ac1a34f )
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 )
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