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Merged
merged 2 commits into from
Jun 6, 2025
Merged

perf: autobump bio/bismark/deduplicate_bismark #4161

merged 2 commits into from
Jun 6, 2025

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Automatic bump of bio/bismark/deduplicate_bismark.

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Automatically approving successfull autobump

@mergify mergify bot merged commit 6de357f into master Jun 6, 2025
7 checks passed
@mergify mergify bot deleted the autobump/bio-bismark-deduplicate_bismark branch June 6, 2025 01:29
@snakemake-bot snakemake-bot mentioned this pull request Jun 6, 2025
Merged
johanneskoester pushed a commit that referenced this pull request Jun 11, 2025
@snakemake-bot
chore(master): release 7.0.0 (#4124)
516186d 
🤖 I have created a release *beep* *boop*
---


##
[7.0.0](v6.2.0...v7.0.0)
(2025-06-11)


### ⚠ BREAKING CHANGES

* trimmomatic wrappers: remove parallel gzip, merge wrappers, added
docs, and code refactoring.
([#4158](#4158))

### Features

* add param for mem_overhead
([#4122](#4122))
([50f8acb](50f8acb))
* add wrapper for MEGAHIT
([#4121](#4121))
([be71b0b](be71b0b))
* Add wrapper for Tandem Repeat Finder (TRF) utility
([#4160](#4160))
([be31100](be31100))
* enable gzip output for bedtools wrappers
([#3642](#3642))
([fc6df02](fc6df02))


### Bug Fixes

* fix 4118
([#4119](#4119))
([00f7aaf](00f7aaf))
* GATK variantrecalibrator wrapper path
([#4126](#4126))
([965df4d](965df4d))
* remove hardcoded shrink type, and fix typos
([#4123](#4123))
([7832d9f](7832d9f))
* trimmomatic wrappers: remove parallel gzip, merge wrappers, added
docs, and code refactoring.
([#4158](#4158))
([c914d68](c914d68))


### Performance Improvements

* autobump bio/bamtools/filter
([#4127](#4127))
([a5f375c](a5f375c))
* autobump bio/bamtools/filter_json
([#4131](#4131))
([da6cc46](da6cc46))
* autobump bio/bamtools/split
([#4130](#4130))
([bcb48e4](bcb48e4))
* autobump bio/bamtools/stats
([#4128](#4128))
([cab52d7](cab52d7))
* autobump bio/bbtools
([#4137](#4137))
([095c7cc](095c7cc))
* autobump bio/bcftools/call
([#4168](#4168))
([49a7824](49a7824))
* autobump bio/bcftools/concat
([#4187](#4187))
([c9e2d7a](c9e2d7a))
* autobump bio/bcftools/filter
([#4197](#4197))
([34f008f](34f008f))
* autobump bio/bcftools/index
([#4192](#4192))
([b9959e9](b9959e9))
* autobump bio/bcftools/merge
([#4174](#4174))
([bbb3c6c](bbb3c6c))
* autobump bio/bcftools/mpileup
([#4178](#4178))
([0c8a6d1](0c8a6d1))
* autobump bio/bcftools/norm
([#4175](#4175))
([7305a0b](7305a0b))
* autobump bio/bcftools/reheader
([#4177](#4177))
([a468bca](a468bca))
* autobump bio/bcftools/sort
([#4183](#4183))
([250b4bc](250b4bc))
* autobump bio/bcftools/stats
([#4194](#4194))
([7525cf1](7525cf1))
* autobump bio/bcftools/view
([#4162](#4162))
([879af38](879af38))
* autobump bio/bedtools/bamtobed
([#4188](#4188))
([7ef5b5d](7ef5b5d))
* autobump bio/bedtools/complement
([#4189](#4189))
([fbea34a](fbea34a))
* autobump bio/bedtools/coveragebed
([#4191](#4191))
([38f8b93](38f8b93))
* autobump bio/bedtools/genomecov
([#4163](#4163))
([923dc25](923dc25))
* autobump bio/bedtools/intersect
([#4198](#4198))
([48042ac](48042ac))
* autobump bio/bedtools/merge
([#4169](#4169))
([46bb04e](46bb04e))
* autobump bio/bedtools/slop
([#4170](#4170))
([c314c49](c314c49))
* autobump bio/bedtools/sort
([#4173](#4173))
([e72641d](e72641d))
* autobump bio/bedtools/split
([#4185](#4185))
([f305aeb](f305aeb))
* autobump bio/bellerophon
([#4180](#4180))
([1064bf7](1064bf7))
* autobump bio/benchmark/chm-eval-sample
([#4179](#4179))
([8b3ecfd](8b3ecfd))
* autobump bio/bgzip
([#4166](#4166))
([a5dcdad](a5dcdad))
* autobump bio/bismark/bam2nuc
([#4181](#4181))
([f88f3f8](f88f3f8))
* autobump bio/bismark/bismark
([#4193](#4193))
([868363e](868363e))
* autobump bio/bismark/bismark_genome_preparation
([#4182](#4182))
([6177626](6177626))
* autobump bio/bismark/bismark_methylation_extractor
([#4165](#4165))
([e509dea](e509dea))
* autobump bio/bismark/bismark2bedGraph
([#4195](#4195))
([1d17cae](1d17cae))
* autobump bio/bismark/bismark2report
([#4196](#4196))
([e884149](e884149))
* autobump bio/bismark/bismark2summary
([#4190](#4190))
([85e4883](85e4883))
* autobump bio/bismark/deduplicate_bismark
([#4161](#4161))
([6de357f](6de357f))
* autobump bio/bowtie2/align
([#4186](#4186))
([36ec656](36ec656))
* autobump bio/bustools/count
([#4138](#4138))
([60fd30a](60fd30a))
* autobump bio/bustools/sort
([#4139](#4139))
([1f5cf71](1f5cf71))
* autobump bio/bustools/text
([#4140](#4140))
([b53856a](b53856a))
* autobump bio/bwa-mem2/mem
([#4172](#4172))
([f77bd3b](f77bd3b))
* autobump bio/bwa/mem
([#4184](#4184))
([2212b96](2212b96))
* autobump bio/bwa/sampe
([#4164](#4164))
([2463d6e](2463d6e))
* autobump bio/bwa/samse
([#4176](#4176))
([3f13ef9](3f13ef9))
* autobump bio/bwa/samxe
([#4171](#4171))
([244efbd](244efbd))
* autobump bio/bwameth/memx
([#4129](#4129))
([0c8667d](0c8667d))
* autobump bio/bwameth/memx
([#4167](#4167))
([978cd77](978cd77))
* autobump bio/cnvkit/export
([#4200](#4200))
([e4b3659](e4b3659))
* autobump bio/cutadapt/pe
([#4142](#4142))
([e764619](e764619))
* autobump bio/cutadapt/se
([#4141](#4141))
([735bfda](735bfda))
* autobump bio/deepvariant
([#4143](#4143))
([4ad6bc7](4ad6bc7))
* autobump bio/delly
([#4203](#4203))
([1bd71f5](1bd71f5))
* autobump bio/diamond/blastp
([#4205](#4205))
([0a4b009](0a4b009))
* autobump bio/diamond/blastx
([#4201](#4201))
([0b8cd8f](0b8cd8f))
* autobump bio/diamond/makedb
([#4202](#4202))
([1bcad8a](1bcad8a))
* autobump bio/entrez/efetch
([#4144](#4144))
([2d09ee0](2d09ee0))
* autobump bio/fastp
([#4145](#4145))
([1e38402](1e38402))
* autobump bio/fastp
([#4207](#4207))
([6cd7e64](6cd7e64))
* autobump bio/freebayes
([#4132](#4132))
([c9749da](c9749da))
* autobump bio/freebayes
([#4206](#4206))
([a2650e2](a2650e2))
* autobump bio/gatk/applybqsr
([#4208](#4208))
([647384e](647384e))
* autobump bio/gatk/applybqsrspark
([#4209](#4209))
([df09bb5](df09bb5))
* autobump bio/gdc-api/bam-slicing
([#4146](#4146))
([68cbc01](68cbc01))
* autobump bio/gdc-api/bam-slicing
([#4211](#4211))
([b2b3643](b2b3643))
* autobump bio/gseapy/gsea
([#4210](#4210))
([5f38932](5f38932))
* autobump bio/hap.py/hap.py
([#4147](#4147))
([86efd6d](86efd6d))
* autobump bio/hisat2/align
([#4213](#4213))
([b349a8c](b349a8c))
* autobump bio/homer/makeTagDirectory
([#4212](#4212))
([fd9c4ff](fd9c4ff))
* autobump bio/lofreq/call
([#4216](#4216))
([d838abd](d838abd))
* autobump bio/lofreq/indelqual
([#4215](#4215))
([53e6cac](53e6cac))
* autobump bio/mapdamage2
([#4148](#4148))
([87d0a10](87d0a10))
* autobump bio/mapdamage2
([#4218](#4218))
([420835f](420835f))
* autobump bio/minimap2/aligner
([#4217](#4217))
([2eb12e1](2eb12e1))
* autobump bio/multiqc
([#4133](#4133))
([9ebdbe9](9ebdbe9))
* autobump bio/ngs-disambiguate
([#4134](#4134))
([015d8ef](015d8ef))
* autobump bio/ngsbits/sampleancestry
([#4149](#4149))
([dff8a93](dff8a93))
* autobump bio/ngsbits/samplesimilarity
([#4150](#4150))
([1362ea7](1362ea7))
* autobump bio/open-cravat/module
([#4219](#4219))
([14f3d59](14f3d59))
* autobump bio/open-cravat/run
([#4220](#4220))
([f68c4dc](f68c4dc))
* autobump bio/paladin/align
([#4224](#4224))
([60a4073](60a4073))
* autobump bio/paladin/index
([#4222](#4222))
([9a49585](9a49585))
* autobump bio/paladin/prepare
([#4226](#4226))
([5ffeda7](5ffeda7))
* autobump bio/picard/markduplicates
([#4221](#4221))
([67ca39e](67ca39e))
* autobump bio/pretext/map
([#4227](#4227))
([d9fef0b](d9fef0b))
* autobump bio/pretext/snapshot
([#4223](#4223))
([6287d9a](6287d9a))
* autobump bio/prinseq-plus-plus
([#4225](#4225))
([d720752](d720752))
* autobump bio/samtools/calmd
([#4244](#4244))
([d7ee375](d7ee375))
* autobump bio/samtools/collate
([#4240](#4240))
([a682845](a682845))
* autobump bio/samtools/depth
([#4231](#4231))
([a7a7101](a7a7101))
* autobump bio/samtools/faidx
([#4243](#4243))
([f7fc7f3](f7fc7f3))
* autobump bio/samtools/fastx
([#4238](#4238))
([17ec481](17ec481))
* autobump bio/samtools/fixmate
([#4248](#4248))
([be8b325](be8b325))
* autobump bio/samtools/flagstat
([#4237](#4237))
([917a816](917a816))
* autobump bio/samtools/idxstats
([#4235](#4235))
([b22e851](b22e851))
* autobump bio/samtools/index
([#4233](#4233))
([3f128ef](3f128ef))
* autobump bio/samtools/markdup
([#4242](#4242))
([58e7715](58e7715))
* autobump bio/samtools/merge
([#4246](#4246))
([a1b731a](a1b731a))
* autobump bio/samtools/mpileup
([#4251](#4251))
([9575f39](9575f39))
* autobump bio/samtools/sort
([#4228](#4228))
([3ce39f0](3ce39f0))
* autobump bio/samtools/stats
([#4229](#4229))
([a390efc](a390efc))
* autobump bio/samtools/view
([#4249](#4249))
([da8e2ad](da8e2ad))
* autobump bio/seqkit
([#4230](#4230))
([731cfb0](731cfb0))
* autobump bio/seqtk
([#4234](#4234))
([d83a202](d83a202))
* autobump bio/snpeff/annotate
([#4250](#4250))
([0d55cf9](0d55cf9))
* autobump bio/snpeff/download
([#4245](#4245))
([9ee55b8](9ee55b8))
* autobump bio/snpsift/annotate
([#4247](#4247))
([0d827da](0d827da))
* autobump bio/snpsift/dbnsfp
([#4232](#4232))
([266def8](266def8))
* autobump bio/snpsift/genesets
([#4241](#4241))
([6476dcc](6476dcc))
* autobump bio/snpsift/gwascat
([#4239](#4239))
([a3b9e06](a3b9e06))
* autobump bio/sortmerna
([#2985](#2985))
([574b4ac](574b4ac))
* autobump bio/sourmash/compute
([#4236](#4236))
([f3abaf2](f3abaf2))
* autobump bio/tabix/query
([#4253](#4253))
([c2937be](c2937be))
* autobump bio/ucsc/twoBitInfo
([#4135](#4135))
([c3cad4f](c3cad4f))
* autobump bio/umis/bamtag
([#4255](#4255))
([d5c415c](d5c415c))
* autobump bio/unicycler
([#4254](#4254))
([2085374](2085374))
* autobump bio/varlociraptor/call-variants
([#4156](#4156))
([7d3f8ef](7d3f8ef))
* autobump bio/varlociraptor/control-fdr
([#4153](#4153))
([ca393f5](ca393f5))
* autobump bio/varlociraptor/estimate-alignment-properties
([#4151](#4151))
([469076e](469076e))
* autobump bio/varlociraptor/preprocess-variants
([#4154](#4154))
([4217362](4217362))
* autobump bio/vembrane/filter
([#4258](#4258))
([be1d8ae](be1d8ae))
* autobump bio/vembrane/table
([#4257](#4257))
([93d47bb](93d47bb))
* autobump bio/vep/annotate
([#4155](#4155))
([e5240f1](e5240f1))
* autobump bio/vep/cache
([#4152](#4152))
([f8af0af](f8af0af))
* autobump bio/vg/giraffe
([#4256](#4256))
([60522de](60522de))
* autobump bio/whatshap/haplotag
([#4157](#4157))
([d55da33](d55da33))
* autobump utils/csvtk
([#4199](#4199))
([c61588a](c61588a))
* autobump utils/datavzrd
([#4204](#4204))
([24ff485](24ff485))
* bump deepvariant version
([#4136](#4136))
([2b488c6](2b488c6))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
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