Releases: snakemake/snakemake-wrappers
Releases · snakemake/snakemake-wrappers
v7.7.0
7.7.0 (2025-10-14)
Features
Bug Fixes
Performance Improvements
- autobump bio/bbtools (#4639) (29e9543)
- autobump bio/encode_fastq_downloader (#4641) (73f2d8c)
- autobump bio/gatk3/baserecalibrator (#4645) (f11dbb9)
- autobump bio/gatk3/indelrealigner (#4644) (d2cb35b)
- autobump bio/gatk3/printreads (#4643) (5954021)
- autobump bio/gatk3/realignertargetcreator (#4646) (baa6e25)
- autobump bio/genomescope (#4642) (bb6e356)
- autobump bio/last/lastal (#4648) (6e940a3)
- autobump bio/last/lastdb (#4647) (5ec863d)
- autobump bio/mehari/annotate-seqvars (#4649) (bf7de05)
- autobump bio/paladin/align (#4650) (83ef7cd)
- autobump bio/paladin/index (#4652) (1b9a197)
- autobump bio/paladin/prepare (#4651) (943dbe6)
- autobump bio/spades/metaspades (#4653) (189beb0)
- autobump bio/vep/plugins (#4655) (0488a2b)
- autobump bio/vsearch (#4654) (65adcaf)
- autobump utils/datavzrd (#4640) (54abde8)
v7.6.1
7.6.1 (2025-10-03)
Performance Improvements
- autobump bio/dragmap/align (#775) (6b8bb26)
- autobump bio/genomepy (#4626) (074d5bc)
- autobump bio/mehari/annotate-seqvars (#4627) (4b77f2c)
- autobump bio/rubic (#3364) (d283645)
- autobump bio/trimmomatic (#4629) (523b456)
- autobump bio/varlociraptor/call-variants (#4630) (f760801)
- autobump bio/varlociraptor/control-fdr (#4633) (0c8c5d9)
- autobump bio/varlociraptor/estimate-alignment-properties (#4635) (aa056dd)
- autobump bio/varlociraptor/preprocess-variants (#4631) (88406f7)
- autobump bio/vembrane/filter (#4634) (3fdc131)
- autobump bio/vembrane/table (#4632) (202cccf)
- autobump geo/overturemaps/download (#4628) (57856cc)
v7.6.0
7.6.0 (2025-09-26)
Features
Bug Fixes
Performance Improvements
- autobump bio/bazam (#4493) (9570a5f)
- autobump bio/bbtools (#4492) (64f3ecf)
- autobump bio/bcftools/call (#4487) (6368005)
- autobump bio/bcftools/concat (#4490) (9e5b7b0)
- autobump bio/bcftools/filter (#4500) (0d53966)
- autobump bio/bcftools/index (#4494) (9ae8bfb)
- autobump bio/bcftools/merge (#4484) (7edd4d4)
- autobump bio/bcftools/mpileup (#4498) (b3ded18)
- autobump bio/bcftools/norm (#4486) (6bee2de)
- autobump bio/bcftools/reheader (#4491) (24b7c38)
- autobump bio/bcftools/sort (#4495) (772201e)
- autobump bio/bcftools/stats (#4485) (4d8fcbf)
- autobump bio/bcftools/view (#4482) (4368cfe)
- autobump bio/bellerophon (#4488) (2e3c18f)
- autobump bio/bowtie2/align (#4497) (1a11b19)
- autobump bio/bustools/sort (#4483) (923c73b)
- autobump bio/bwa-mem2/mem (#4496) (9e68419)
- autobump bio/bwa/mem (#4489) (57418a1)
- autobump bio/bwameth/memx (#4499) (77d8897)
- autobump bio/delly (#4502) (1bbdf4a)
- autobump bio/fastqc (#4503) (377bf08)
- autobump bio/fgbio/annotatebamwithumis (#4507) (8d9b283)
- autobump bio/fgbio/collectduplexseqmetrics (#4506) (3c61f67)
- autobump bio/filtlong (#4505) (cd3d276)
- autobump bio/freebayes (#4504) (92ad026)
- autobump bio/gatk/applybqsr (#4522) (a8d0a72)
- autobump bio/gatk/applybqsrspark (#4546) (5fc9cd5)
- autobump bio/gatk/applyvqsr (#4535) (aa13bae)
- autobump bio/gatk/baserecalibrator (#4534) (9262a33)
- autobump bio/gatk/baserecalibratorspark (#4514) (a5b751f)
- autobump bio/gatk/calculatecontamination (#4537) (a4b2bde)
- autobump bio/gatk/callcopyratiosegments (#4531) (0eef601)
- autobump bio/gatk/cleansam (#4512) (993eb62)
- autobump bio/gatk/collectalleliccounts (#4510) (a7720c7)
- autobump bio/gatk/collectreadcounts (#4516) (12be359)
- autobump bio/gatk/combinegvcfs (#4508) (2914607)
- autobump bio/gatk/denoisereadcounts (#4515) (3dbc217)
- autobump bio/gatk/depthofcoverage (#4542) (f7f412e)
- autobump bio/gatk/estimatelibrarycomplexity (#4532) (893f523)
- autobump bio/gatk/filtermutectcalls (#4544) (7e74f7b)
- autobump bio/gatk/genomicsdbimport (#4526) (659a78d)
- autobump bio/gatk/genotypegvcfs (#4530) (5b3595c)
- autobump bio/gatk/getpileupsummaries (#4513) (e3679c0)
- autobump bio/gatk/haplotypecaller (#4533) (33817fc)
- autobump bio/gatk/intervallisttobed ([#4545](https://github.com/snakemake/snak...
v7.5.0
v7.4.0
v7.3.0
7.3.0 (2025-09-17)
Features
Bug Fixes
- Add fallback to FTP if HTTPS cache download fails for vep-cache (#4474) (eb6afba)
- bug when rescaling BAM (#3687) (991f553)
Performance Improvements
- autobump bio/agat (#4384) (6787322)
- autobump bio/arriba (#4427) (8c83380)
- autobump bio/bbtools (#4385) (22fbb97)
- autobump bio/bedtools/bamtobed (#4341) (5729662)
- autobump bio/bedtools/complement (#4345) (16fdf5e)
- autobump bio/bedtools/coveragebed (#4328) (cfcacc9)
- autobump bio/bedtools/genomecov (#4335) (2f19a2c)
- autobump bio/bedtools/intersect (#4337) (8182f18)
- autobump bio/bedtools/merge (#4339) (43fb28b)
- autobump bio/bedtools/slop (#4330) (73aa7fb)
- autobump bio/bedtools/sort (#4322) (deb88ba)
- autobump bio/bedtools/split (#4344) (16c0956)
- autobump bio/bellerophon (#4324) (d89db19)
- autobump bio/benchmark/chm-eval-sample (#4338) (d83a1d1)
- autobump bio/bgzip (#4325) (1b35337)
- autobump bio/bismark/bam2nuc (#4336) (339ee3e)
- autobump bio/bismark/bam2nuc (#4412) (a7f64e3)
- autobump bio/bismark/bismark (#4346) (1f578f6)
- autobump bio/bismark/bismark (#4410) (a4d45ec)
- autobump bio/bismark/bismark_genome_preparation (#4340) (2e0c11f)
- autobump bio/bismark/bismark_genome_preparation (#4409) (0be0eb9)
- autobump bio/bismark/bismark_methylation_extractor (#4342) (0b7b228)
- autobump bio/bismark/bismark_methylation_extractor (#4408) (e6f32f1)
- autobump bio/bismark/bismark2bedGraph (#4327) (b57419f)
- autobump bio/bismark/bismark2bedGraph (#4405) (601301f)
- autobump bio/bismark/bismark2report (#4323) (5c06556)
- autobump bio/bismark/bismark2report (#4411) (e8cbdb4)
- autobump bio/bismark/bismark2summary (#4331) (0980889)
- autobump bio/bismark/bismark2summary (#4406) (f036911)
- autobump bio/bismark/deduplicate_bismark (#4343) (0d15def)
- autobump bio/bismark/deduplicate_bismark (#4407) (c083000)
- autobump bio/blast/blastn (#4421) (4f8c073)
- autobump bio/blast/makeblastdb (#4422) (4e0afea)
- autobump bio/bowtie2/align (#4333) (5d41bd4)
- autobump bio/busco (#4312) (01668b0)
- autobump bio/bwa-mem2/mem (#4329) (11b6a92)
- autobump bio/bwa/mem (#4332) (7e4e103)
- autobump bio/bwa/mem (#4428) (b8ab92c)
- autobump bio/bwa/sampe (#4321) (e2be272)
- autobump bio/bwa/samse (#4347) (14a7775)
- autobump bio/bwa/samxe (#4334) (e02428f)
- autobump bio/bwameth/index (#4391) (8344109)
- autobump bio/bwameth/index (#4420) (61d3fad)
- autobump bio/b...
v7.2.0
7.2.0 (2025-07-04)
Features
- add mehari wrappers (#4274) (0d2d267)
- Agat (#4285) (20748cc)
- Pyfaidx regions (#4299) (b980196)
- rasterio - clipping of Cloud Optimized GeoTIFF (#4286) (7dd85d9)
- Updated trf to 4.10.0rc2 (#4297) (7a8a3f2)
Bug Fixes
Performance Improvements
- autobump bio/agat (#4302) (8bc6320)
- autobump bio/bbtools (#4288) (0b9f9b7)
- autobump bio/bwa-mem2/index (#4303) (5be7745)
- autobump bio/bwa-mem2/mem (#4304) (00573fb)
- autobump bio/bwa-mem2/mem-samblaster (#4305) (76f261c)
- autobump bio/bwameth/index (#4306) (1e27c40)
- autobump bio/freebayes (#4289) (beed7c7)
- autobump bio/last/lastal (#4291) (44bb426)
- autobump bio/last/lastdb (#4290) (3c1083e)
- autobump bio/mehari/annotate-seqvars (#4307) (8819087)
- autobump bio/picard/collectinsertsizemetrics (#4292) (5785f6f)
- autobump bio/sourmash/compute (#4309) (361ea21)
- autobump bio/trf (#4293) (568a6d3)
- autobump bio/ucsc/bedGraphToBigWig (#4296) (fd977bd)
- autobump bio/ucsc/genePredToBed (#4295) (a9a9597)
- autobump bio/ucsc/gtfToGenePred (#4294) (3bd7f08)
- autobump bio/vep/annotate (#4311) (a3802b3)
- autobump bio/vep/cache (#4310) (818295e)
- autobump geo/rasterio/clip-geotiff (#4308) (db4661f)
v7.1.0
7.1.0 (2025-06-20)
Features
Bug Fixes
Performance Improvements
- autobump bio/bismark/bismark_methylation_extractor (#4260) (bfd4627)
- autobump bio/encode_fastq_downloader (#4263) (534231d)
- autobump bio/fastp (#4275) (a315cff)
- autobump bio/gatk3/baserecalibrator (#4268) (3941eec)
- autobump bio/gatk3/indelrealigner (#4266) (7142888)
- autobump bio/gatk3/printreads (#4267) (a70ac2a)
- autobump bio/gatk3/realignertargetcreator (#4265) (7aac10d)
- autobump bio/gfatools (#4264) (6df1c85)
- autobump bio/igv-reports (#4214) (b93892b)
- autobump bio/mapdamage2 (#4269) (677d564)
- autobump bio/minimap2/aligner (#4276) (2944f38)
- autobump bio/minimap2/index (#4277) (d92345b)
- autobump bio/reference/ensembl-variation (#4278) (5b55c94)
- autobump bio/spades/metaspades (#4270) (2d1b106)
- autobump bio/tabix/index (#4252) (0152771)
- autobump bio/trf (#4271) (1e80067)
- autobump bio/ucsc/faToTwoBit (#4281) (0037df1)
- autobump bio/ucsc/twoBitInfo (#4279) (e0048ce)
- autobump bio/ucsc/twoBitToFa (#4280) (ff31ef7)
- autobump bio/vembrane/filter (#4282) (870f1b0)
- autobump bio/vembrane/table (#4283) (d4797c9)
- autobump bio/vep/plugins (#4272) (7c47ce0)
- autobump bio/whatshap/haplotag (#4273) (cd59f63)
- autobump utils/datavzrd (#4262) (aa0dc22)
v7.0.0
7.0.0 (2025-06-11)
⚠ BREAKING CHANGES
- trimmomatic wrappers: remove parallel gzip, merge wrappers, added docs, and code refactoring. (#4158)
Features
- add param for mem_overhead (#4122) (50f8acb)
- add wrapper for MEGAHIT (#4121) (be71b0b)
- Add wrapper for Tandem Repeat Finder (TRF) utility (#4160) (be31100)
- enable gzip output for bedtools wrappers (#3642) (fc6df02)
Bug Fixes
- fix 4118 (#4119) (00f7aaf)
- GATK variantrecalibrator wrapper path (#4126) (965df4d)
- remove hardcoded shrink type, and fix typos (#4123) (7832d9f)
- trimmomatic wrappers: remove parallel gzip, merge wrappers, added docs, and code refactoring. (#4158) (c914d68)
Performance Improvements
- autobump bio/bamtools/filter (#4127) (a5f375c)
- autobump bio/bamtools/filter_json (#4131) (da6cc46)
- autobump bio/bamtools/split (#4130) (bcb48e4)
- autobump bio/bamtools/stats (#4128) (cab52d7)
- autobump bio/bbtools (#4137) (095c7cc)
- autobump bio/bcftools/call (#4168) (49a7824)
- autobump bio/bcftools/concat (#4187) (c9e2d7a)
- autobump bio/bcftools/filter (#4197) (34f008f)
- autobump bio/bcftools/index (#4192) (b9959e9)
- autobump bio/bcftools/merge (#4174) (bbb3c6c)
- autobump bio/bcftools/mpileup (#4178) (0c8a6d1)
- autobump bio/bcftools/norm (#4175) (7305a0b)
- autobump bio/bcftools/reheader (#4177) (a468bca)
- autobump bio/bcftools/sort (#4183) (250b4bc)
- autobump bio/bcftools/stats (#4194) (7525cf1)
- autobump bio/bcftools/view (#4162) (879af38)
- autobump bio/bedtools/bamtobed (#4188) (7ef5b5d)
- autobump bio/bedtools/complement (#4189) (fbea34a)
- autobump bio/bedtools/coveragebed (#4191) (38f8b93)
- autobump bio/bedtools/genomecov (#4163) (923dc25)
- autobump bio/bedtools/intersect (#4198) (48042ac)
- autobump bio/bedtools/merge (#4169) (46bb04e)
- autobump bio/bedtools/slop (#4170) (c314c49)
- autobump bio/bedtools/sort (#4173) (e72641d)
- autobump bio/bedtools/split (#4185) (f305aeb)
- autobump bio/bellerophon (#4180) (1064bf7)
- autobump bio/benchmark/chm-eval-sample (#4179) (8b3ecfd)
- autobump bio/bgzip (#4166) (a5dcdad)
- autobump bio/bismark/bam2nuc (#4181) (f88f3f8)
- autobump bio/bismark/bismark (#4193) (868363e)
- autobump bio/bismark/bismark_genome_preparation (#4182) (6177626)
- autobump bio/bismark/bismark_methylation_extractor (#4165) (e509dea)
- autobump bio/bismark/bismark2bedGraph (#4195) (1d17cae)
- autobump bio/bismark/bismark2report (#4196) (e884149)
- autobump bio/bismark/bismark2summary (#4190) (85e4883)
- autobump bio/bismark/deduplicate_bismark (#4161) (6de357f)
- autobump bio/bowtie2/align (#4186) ([36ec656](36ec656e51eb7cb9665c58c09...