chore(main): release 0.1.0

[tedil]

🤖 I have created a release beep boop

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) (feat!: use snakemake tmpdir resource (#319) #320)
• merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) (refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) #315)
• merge {variant,wgs_{sv,cnv}}_calling_export into varfish_export (#308) (feat!: merge {variant,wgs_{sv,cnv}}_calling_export into varfish_export (#308) #309)
• move "bcftools roh" as report in variant_calling (#310) (refactor!: move "bcftools roh" as report in variant_calling (#310) #311)
• rename targeted_seq_cnv_calling to sv_calling_targeted (#305) (refactor!: rename targeted_seq_cnv_calling to sv_calling_targeted (#305) #306)
• rename helper_gcnv_model_target_seq to helper_gcnv_targeted (#303) (refactor!: 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 (#288) (#290) (125b601)
• replacing custom coverage QC scripts with "alfred qc" (#481) (#482) (ae8fe98)
• Somatic cnv checking (#426) (18217bc)
• 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)
• use snakemake tmpdir resource (#319) (#320) (c8512b0)

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

• not using parallel --workdir (#328) (#332) (4cd1531)

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)

---

This PR was generated with Release Please. See documentation.

[coveralls]

coverage: 85.999%. remained the same
when pulling b14c08a on release-please--branches--main
into be0ac09 on main.

[coveralls]

coverage: 86.001%. remained the same
when pulling d54e01e on release-please--branches--main
into 4fb8d8d on main.

[Nicolai-vKuegelgen]

This is pinned as a release to have a baseline of the current snappy version.

LGTM

[tedil]

🤖 Created releases:

• v0.1.0
  🌻