Releases: snakemake/snakemake-wrappers
Releases · snakemake/snakemake-wrappers
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...
v6.2.0
v6.1.1
6.1.1 (2025-05-16)
Performance Improvements
- autobump bio/bbtools (#4088) (0449fb2)
- autobump bio/freebayes (#4091) (1a3246f)
- autobump bio/genomepy (#4109) (d28e8f4)
- autobump bio/reference/ensembl-biomart-table (#3348) (668257f)
- autobump bio/sourmash/compute (#4092) (96c6e2f)
- autobump bio/spades/metaspades (#4093) (f79580f)
- autobump bio/subread/featurecounts (#4094) (547a927)
- autobump bio/taxonkit (#4095) (7e62290)
- autobump bio/ucsc/bedGraphToBigWig (#4110) (53baae2)
- autobump bio/unicycler (#4096) (5d13680)
- autobump bio/varlociraptor/call-variants (#4114) (04b10f8)
- autobump bio/varlociraptor/control-fdr (#4115) (f0d85e2)
- autobump bio/varlociraptor/estimate-alignment-properties (#4113) (71a2bed)
- autobump bio/varlociraptor/preprocess-variants (#4117) (985cdf9)
- autobump bio/vcftools/filter (#4116) (bd5d486)
- autobump bio/vep/annotate (#4112) (65b04c6)
- autobump bio/vep/cache (#4111) (3848d50)
- autobump bio/vg/construct (#4097) (8913e45)
- autobump bio/vg/ids (#4101) (6fc60ca)
- autobump bio/vg/kmers (#4102) (3ed9484)
- autobump bio/vg/merge (#4098) (6030ce7)
- autobump bio/vg/prune (#4100) (bff067e)
- autobump bio/vg/sim (#4099) (2ea8db2)
- autobump utils/cairosvg (#4107) (7f6f15e)
- autobump utils/datavzrd (#4090) (1f1edc0)
- autobump utils/datavzrd (#4108) (f050aad)
v6.1.0
v6.0.2
6.0.2 (2025-05-02)
Performance Improvements
- autobump bio/bustools/count (#4037) (95c8497)
- autobump bio/bustools/sort (#4035) (32ccc8a)
- autobump bio/bustools/text (#4036) (1897a3b)
- autobump bio/freebayes (#4040) (d2967d9)
- autobump bio/freebayes (#4048) (4698130)
- autobump bio/gatk/applybqsr (#4071) (006f004)
- autobump bio/gatk/applybqsrspark (#4077) (9e9f99d)
- autobump bio/gatk/applyvqsr (#4069) (52b8fe4)
- autobump bio/gatk/baserecalibrator (#4075) (3a0a28d)
- autobump bio/gatk/baserecalibratorspark (#4082) (023a266)
- autobump bio/gatk/calculatecontamination (#4057) (12077d7)
- autobump bio/gatk/callcopyratiosegments (#4068) (f77af70)
- autobump bio/gatk/cleansam (#4052) (b1b978e)
- autobump bio/gatk/collectalleliccounts (#4060) (8cf95c7)
- autobump bio/gatk/collectreadcounts (#4076) (2a0352b)
- autobump bio/gatk/combinegvcfs (#4058) (d06a4cb)
- autobump bio/gatk/denoisereadcounts (#4056) (5916cd0)
- autobump bio/gatk/depthofcoverage (#4073) (34f4250)
- autobump bio/gatk/estimatelibrarycomplexity (#4061) (9184245)
- autobump bio/gatk/filtermutectcalls (#4064) (f16428d)
- autobump bio/gatk/genomicsdbimport (#4051) (85187d8)
- autobump bio/gatk/genotypegvcfs (#4074) (66d7223)
- autobump bio/gatk/getpileupsummaries (#4055) (ae67a18)
- autobump bio/gatk/haplotypecaller (#4054) (056046f)
- autobump bio/gatk/intervallisttobed (#4067) (a8e8946)
- autobump bio/gatk/learnreadorientationmodel (#4053) (0277f44)
- autobump bio/gatk/leftalignandtrimvariants (#4072) (681e71b)
- autobump bio/gatk/markduplicatesspark (#4070) (91df6c2)
- autobump bio/gatk/modelsegments (#4080) (58700da)
- autobump bio/gatk/mutect (#4066) (3446daa)
- autobump bio/gatk/printreadsspark (#4063) (1d4d052)
- autobump bio/gatk/scatterintervalsbyns (#4059) (4376cd0)
- autobump bio/gatk/selectvariants (#4049) (7b6a578)
- autobump bio/gatk/splitintervals (#4065) (14f2d1f)
- autobump bio/gatk/splitncigarreads (#4081) (0ee053f)
- autobump bio/gatk/variantannotator (#4078) (b355de4)
- autobump bio/gatk/varianteval (#4062) (bc67ec5)
- autobump bio/gatk/variantfiltration (#4050) (98916ce)
- autobump bio/gatk/variantrecalibrator (#4079) (6faba35)
- autobump bio/gatk/variantstotable (#4083) (4e6286a)
- autobump bio/minimap2/aligner (#4042) (81e2033)
- autobump bio/minimap2/index (#4041) (881d956)
- autobump bio/open-cravat/module (#4044) (5443274)
- autobump bio/open-cravat/run (#4043) (ec23c45)
- autobump bio/tximport (#4045) (3fc02ea)
- autobump bio/ucsc/faToTwoBit (#4084) ([62344c0](62344c0d6e...
v6.0.1
6.0.1 (2025-04-18)
Performance Improvements
- autobump bio/bwa-mem2/mem (#4011) (26427cf)
- autobump bio/bwa-meme/mem (#4010) (9b29136)
- autobump bio/bwa-memx/mem (#4015) (a3f052f)
- autobump bio/bwa/mem (#4014) (9893f31)
- autobump bio/bwa/sampe (#4012) (20a4ea0)
- autobump bio/bwa/samse (#4013) (460e426)
- autobump bio/bwa/samxe (#4009) (f8357cd)
- autobump bio/fastp (#4016) (32fb271)
- autobump bio/picard/addorreplacereadgroups (#4027) (48b9bfb)
- autobump bio/picard/bedtointervallist (#4029) (a49cf4d)
- autobump bio/picard/collectalignmentsummarymetrics (#4032) (4282aa2)
- autobump bio/picard/collectgcbiasmetrics (#4031) (c4de167)
- autobump bio/picard/collecthsmetrics (#4021) (82ed4fe)
- autobump bio/picard/collectinsertsizemetrics (#4020) (9e30fc8)
- autobump bio/picard/collectmultiplemetrics (#4019) (bdd6f41)
- autobump bio/picard/collectrnaseqmetrics (#4023) (ce66ef8)
- autobump bio/picard/collecttargetedpcrmetrics (#4018) (caa5ea3)
- autobump bio/picard/createsequencedictionary (#4028) (bb47247)
- autobump bio/picard/markduplicates (#4025) (fe41f5a)
- autobump bio/picard/mergesamfiles (#4026) (e55dc7e)
- autobump bio/picard/mergevcfs (#4024) (eda2889)
- autobump bio/picard/revertsam (#4022) (7f9382b)
- autobump bio/picard/samtofastq (#4030) (ee1a07b)
- autobump bio/picard/sortsam (#4017) (c987d49)
- autobump bio/vg/giraffe (#4033) (f6560f0)
- autobump bio/whatshap/haplotag (#4034) (f6b55be)
- Update datavzrd wrapper to 2.53.1 (#4007) (c7672a8)
v6.0.0
6.0.0 (2025-04-11)
⚠ BREAKING CHANGES
- bismark main alignment wrapper to best practices (#3974)
- handle all the bismark_genome_preparation cli quirks (#3973)
Bug Fixes
- bismark main alignment wrapper to best practices (#3974) (b368e93)
- handle all the bismark_genome_preparation cli quirks (#3973) (628d21c)
Performance Improvements
- autobump bio/bwa/mem (#3982) (1abfc8e)
- autobump bio/deseq2/deseqdataset (#3977) (9988759)
- autobump bio/encode_fastq_downloader (#3984) (d551b05)
- autobump bio/fgbio/annotatebamwithumis (#3990) (91a378d)
- autobump bio/fgbio/callmolecularconsensusreads (#3986) (5c7cb57)
- autobump bio/fgbio/collectduplexseqmetrics (#3987) (b8dfc5f)
- autobump bio/fgbio/filterconsensusreads (#3988) (0f528d6)
- autobump bio/fgbio/groupreadsbyumi (#3989) (3b72318)
- autobump bio/fgbio/setmateinformation (#3985) (7e954b9)
- autobump bio/gatk3/baserecalibrator (#3992) (3ea92a0)
- autobump bio/gatk3/indelrealigner (#3994) (18e0851)
- autobump bio/gatk3/printreads (#3991) (b20391d)
- autobump bio/gatk3/realignertargetcreator (#3995) (5fefdae)
- autobump bio/gdc-api/bam-slicing (#3979) (c32b1a8)
- autobump bio/gseapy/gsea (#3993) (1f9f33c)
- autobump bio/last/lastal (#3996) (e8d7aeb)
- autobump bio/last/lastdb (#3997) (d61ab4f)
- autobump bio/mapdamage2 (#3998) (427ef9e)
- autobump bio/mashmap (#3999) (6b383e4)
- autobump bio/pretext/graph (#4001) (65b6550)
- autobump bio/salmon/decoys (#4004) (3f5049b)
- autobump bio/salmon/quant (#4002) (8ad15b9)
- autobump bio/spades/metaspades (#4003) (48809df)
- autobump bio/sra-tools/fasterq-dump (#3615) (a24c7dd)
- autobump bio/vep/plugins (#4005) (10fe869)
- autobump bio/vg/giraffe (#4006) (0fff7ae)
- autobump bio/whatshap/haplotag (#3980) (65b5db1)
- autobump utils/datavzrd (#3978) (1240480)
- autobump utils/datavzrd (#3983) (4637b4d)
v5.10.0
5.10.0 (2025-03-28)
Features
- Add wrapper for miller (#3850) (6e164d7)
- use ensembl-sequence https download links, allow .gz output, check links without downloading (#3852) (7e90e8a)
Bug Fixes
Performance Improvements
- autobump bio/arriba (#3853) (7ec8701)
- autobump bio/bazam (#3743) (9baf3d9)
- autobump bio/bazam (#3872) (5c39df0)
- autobump bio/bbtools (#3731) (ca38c0a)
- autobump bio/bbtools (#3876) (9795342)
- autobump bio/bcftools/call (#3746) (e4e2fba)
- autobump bio/bcftools/call (#3868) (ae9403d)
- autobump bio/bcftools/concat (#3740) (6dbe722)
- autobump bio/bcftools/concat (#3866) (e48207b)
- autobump bio/bcftools/filter (#3737) (2bc43be)
- autobump bio/bcftools/filter (#3860) (55a01ce)
- autobump bio/bcftools/index (#3730) (b33e503)
- autobump bio/bcftools/index (#3858) (d096563)
- autobump bio/bcftools/merge (#3744) (28512b2)
- autobump bio/bcftools/merge (#3874) (53a4263)
- autobump bio/bcftools/mpileup (#3741) (b0ca3e9)
- autobump bio/bcftools/mpileup (#3862) (532ecbe)
- autobump bio/bcftools/norm (#3745) (96acc16)
- autobump bio/bcftools/norm (#3867) (5aa7b0d)
- autobump bio/bcftools/reheader (#3732) (a686711)
- autobump bio/bcftools/reheader (#3871) (ce22ff0)
- autobump bio/bcftools/sort (#3734) (eaf5c8c)
- autobump bio/bcftools/sort (#3863) (944727a)
- autobump bio/bcftools/stats (#3747) (2d5a32f)
- autobump bio/bcftools/stats (#3869) (5e3a295)
- autobump bio/bcftools/view (#3748) (ae31135)
- autobump bio/bcftools/view (#3855) (80cc06f)
- autobump bio/bellerophon (#3742) (ee2b2c9)
- autobump bio/bellerophon (#3865) (66b137d)
- autobump bio/bowtie2/align (#3733) (fc2fbe9)
- autobump bio/bowtie2/align (#3854) (4df3d4d)
- autobump bio/bustools/sort (#3739) (c2c7d4d)
- autobump bio/bustools/sort (#3877) (c07344b)
- autobump bio/bwa-mem2/mem (#3735) (65858e6)
- autobump bio/bwa-mem2/mem (#3861) (36aa434)
- autobump bio/bwa/aln (#3859) (5375694)
- autobump bio/bwa/index (#3856) (79eec23)
- autobump bio/bwa/mem (#3736) (f57af1a)
- autobump bio/bwa/mem (#3857) (a529b48)
- autobump bio/bwa/mem-samblaster (#3870) (fabd4dc)
- autobump bio/bwa/sampe (#3873) (368923b)
- autobump bio/bwa/samse (#3875) (a8d6613)
- autobump bio/bwa/samxe (#3864) (c9b7084)
- autobump bio/delly (#3749) ([b4aac11](b4aac11...
v5.9.0
5.9.0 (2025-03-14)
Features
- add
overturemapscli wrapper (#3689) (f2e6355) - add
pygadmwrapper for geo spatial items (#3711) (c72eeb0) - Add jackhmmer wrapper from hmmer package. (#3714) (cef598e)
- Bump meryl version (#3727) (cf6dd6c)
- grouping of wrappers and meta-wrappers by scientific field (#3717) (d3071e8)
Bug Fixes
Performance Improvements
- autobump bio/bbtools (#3691) (96efbe7)
- autobump bio/busco (#3718) (07bdd19)
- autobump bio/bwa/mem (#3692) (92caa80)
- autobump bio/deseq2/deseqdataset (#3693) (8b68685)
- autobump bio/fgbio/annotatebamwithumis (#3698) (530e379)
- autobump bio/fgbio/callmolecularconsensusreads (#3697) (4fd7929)
- autobump bio/fgbio/collectduplexseqmetrics (#3699) (eff79ba)
- autobump bio/fgbio/filterconsensusreads (#3696) (8a908b1)
- autobump bio/fgbio/groupreadsbyumi (#3695) (46404bb)
- autobump bio/fgbio/setmateinformation (#3700) (1860fd7)
- autobump bio/gseapy/gsea (#3701) (5107aa1)
- autobump bio/last/lastal (#3722) (2fa082b)
- autobump bio/last/lastdb (#3721) (144cc02)
- autobump bio/picard/collectinsertsizemetrics (#3703) (8572022)
- autobump bio/reference/ensembl-mysql-table (#3724) (20c3ff3)
- autobump bio/seqkit (#3725) (f30e212)
- autobump bio/taxonkit (#3726) (a63d5a6)
- autobump bio/tximport (#3704) (650ed53)
- autobump bio/ucsc/gtfToGenePred (#3705) (1fdb394)
- autobump bio/varlociraptor/call-variants (#3710) (c3f4e44)
- autobump bio/varlociraptor/control-fdr (#3707) (8ca4adb)
- autobump bio/varlociraptor/estimate-alignment-properties (#3708) (d42def9)
- autobump bio/varlociraptor/preprocess-variants (#3709) (134d1e5)
- autobump bio/vg/giraffe (#3706) (5d06651)
- autobump geo/overturemaps/download (#3702) (9b06df4)
- autobump geo/pygadm/item (#3723) (069069a)
- autobump utils/csvtk (#3719) (78f51eb)
- autobump utils/datavzrd (#3694) (63328e6)
- autobump utils/datavzrd (#3720) (5fcc5ec)
- don't run code quality checks if only
CHANGELOG.mdmodified (#3713) (edb8130)