Commits on Jun 11, 2025

1. feat: Add wrapper for Tandem Repeat Finder (TRF) utility (#4160) …

   This PR provides support of executing TRF command line utility
   (https://prefix.dev/channels/bioconda/packages/trf) through Snakemake
   using Snakemake wrappers. On top of basic TRF feature(s) this wrapper
   additionally makes it easy for users to write Snakemake rules by
   providing following things:
   - In case user doesn't provide any parameters it automatically sets to
   recommended defaults by the TRF author as on the
   website(https://tandem.bu.edu/trf/help) and allows users to right a bare
   minimum Snakemake rule.
   - Raises errors or warning in case the parameter value or flag with
   options value is set to that not allowed by the author.
   - It filters or recognizes some mistakes and raise errors or warning
   based on that:
     - Error in case a known flag is mistyped like -m tp *m with feedback.
   - Warning and ignoring unknown flags if tried to entered like -) -Y etc.
   - Supporting multiple options for option value flag, -l20, -l 20 and
   -l=20.
   - In case user provides partial parameters list, it use recommended
   defaults with updates to those parameters which user provided
   specifically.
   - Handles missing log files gracefully.
   - Support to print the directory contents on Screen once output has been
   ready.
   - Has logging configured for debug, info mode etc.
   - Allows fasta format only as per snakemake wrapper utils:
   https://github.com/snakemake/snakemake-wrapper-utils/blob/master/snakemake_wrapper_utils/snakemake.py
   - Have basic integration tests in place with various rule scenarios. 
   - Updated meta for related documentation.  
   
   ### QC
   * [X] I confirm that I have followed the [documentation for contributing
   to
   `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).
   
   While the contributions guidelines are more extensive, please
   particularly ensure that:
   * [X] `test.py` was updated to call any added or updated example rules
   in a `Snakefile` -> _**yes, but in test-wrappers.py**_
   * [X] `input:` and `output:` file paths in the rules can be chosen
   arbitrarily
   * [X] wherever possible, command line arguments are inferred and set
   automatically (e.g. based on file extensions in `input:` or `output:`)
   * [ ] temporary files are either written to a unique hidden folder in
   the working directory, or (better) stored where the Python function
   `tempfile.gettempdir()` points to -> _**Not applicable in my case.**_
   * [X] the `meta.yaml` contains a link to the documentation of the
   respective tool or command under `url:`
   * [X] conda environments use a minimal amount of channels and packages,
   in recommended ordering
   
   
   <!-- This is an auto-generated comment: release notes by coderabbit.ai
   -->
   ## Summary by CodeRabbit
   
   - **New Features**
   - Added a Snakemake wrapper for the Tandem Repeat Finder (TRF) tool,
   enabling automated detection of tandem repeats in DNA sequences.
   - Provided environment configuration files for reproducible setup on
   Linux platforms.
   - Included metadata and documentation for wrapper usage, parameters, and
   outputs.
   
   - **Tests**
   - Introduced comprehensive test workflows and sample data to validate
   the TRF wrapper under various scenarios, including parameter variations
   and error handling.
   <!-- end of auto-generated comment: release notes by coderabbit.ai -->
   
   ---------
   
   Co-authored-by: rohan-ibn-tariq <[email protected]>

   

   rohan-ibn-tariq and rohan-ibn-tariq authored Jun 11, 2025
   Configuration menu

   • View commit details
   • Copy full SHA for be31100
   • Browse repository at this point

   Copy the full SHA

   be31100 View commit details

   Browse the repository at this point in the history

2. fix!: trimmomatic wrappers: remove parallel gzip, merge wrappers, add… …

   …ed docs, and code refactoring. (#4158)
   
   <!-- Ensure that the PR title follows conventional commit style (<type>:
   <description>)-->
   <!-- Possible types are here:
   https://github.com/commitizen/conventional-commit-types/blob/master/index.json
   -->
   
   <!-- Add a description of your PR here-->
   Current parallel compression/decompression with `pigz` is no longer
   supported in latest versions of `Trimmomatic` and it breaks MultiQC
   reporting. Since it seems that the next version of Trimmomatic will have
   [parallel compression](
   
   usadellab/Trimmomatic@7220eba),
   this issues removes it, bumps versions, refactors code, merges the two
   PE/SE wrappers, and iproves docs.
   
   Closes #778 
   Closes #869 
   Fixes #961 
   
   ### QC
   <!-- Make sure that you can tick the boxes below. -->
   
   * [x] I confirm that I have followed the [documentation for contributing
   to
   `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).
   
   While the contributions guidelines are more extensive, please
   particularly ensure that:
   * [x] `test.py` was updated to call any added or updated example rules
   in a `Snakefile`
   * [x] `input:` and `output:` file paths in the rules can be chosen
   arbitrarily
   * [x] wherever possible, command line arguments are inferred and set
   automatically (e.g. based on file extensions in `input:` or `output:`)
   * [x] temporary files are either written to a unique hidden folder in
   the working directory, or (better) stored where the Python function
   `tempfile.gettempdir()` points to
   * [x] the `meta.yaml` contains a link to the documentation of the
   respective tool or command under `url:`
   * [x] conda environments use a minimal amount of channels and packages,
   in recommended ordering
   
   
   <!-- This is an auto-generated comment: release notes by coderabbit.ai
   -->
   ## Summary by CodeRabbit
   
   - **New Features**
   - Introduced unified configuration and metadata files for running
   Trimmomatic, supporting both paired-end and single-end workflows with
   various input/output formats.
   - Added a new wrapper script to streamline Trimmomatic execution within
   Snakemake workflows.
   
   - **Refactor**
   - Consolidated multiple environment and metadata files into a single set
   for easier management and reproducibility.
   - Unified Snakemake rules for Trimmomatic into a single, comprehensive
   Snakefile covering all compression and read-type combinations.
   - Removed legacy single-end and paired-end specific environment and
   metadata files along with deprecated wrapper scripts.
   
   - **Tests**
   - Simplified and consolidated test coverage for paired-end workflows;
   removed separate single-end tests.
   <!-- end of auto-generated comment: release notes by coderabbit.ai -->

   

   fgvieira authored Jun 11, 2025
   Configuration menu

   • View commit details
   • Copy full SHA for c914d68
   • Browse repository at this point

   Copy the full SHA

   c914d68 View commit details

   Browse the repository at this point in the history

3. fix: GATK variantrecalibrator wrapper path (#4126) …

   <!-- Ensure that the PR title follows conventional commit style (<type>:
   <description>)-->
   <!-- Possible types are here:
   https://github.com/commitizen/conventional-commit-types/blob/master/index.json
   -->
   
   <!-- Add a description of your PR here-->
   Fixes #4125 
   
   ### QC
   <!-- Make sure that you can tick the boxes below. -->
   
   * [x] I confirm that I have followed the [documentation for contributing
   to
   `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).
   
   While the contributions guidelines are more extensive, please
   particularly ensure that:
   * [x] `test.py` was updated to call any added or updated example rules
   in a `Snakefile`
   * [x] `input:` and `output:` file paths in the rules can be chosen
   arbitrarily
   * [x] wherever possible, command line arguments are inferred and set
   automatically (e.g. based on file extensions in `input:` or `output:`)
   * [x] temporary files are either written to a unique hidden folder in
   the working directory, or (better) stored where the Python function
   `tempfile.gettempdir()` points to
   * [x] the `meta.yaml` contains a link to the documentation of the
   respective tool or command under `url:`
   * [x] conda environments use a minimal amount of channels and packages,
   in recommended ordering
   
   
   <!-- This is an auto-generated comment: release notes by coderabbit.ai
   -->
   ## Summary by CodeRabbit
   
   - **Chores**
   - Updated the source path for the wrapper used in the variant
   recalibration workflow.
   - Improved remote resource access by updating URLs and fetching methods
   in the variant recalibration tests.
   <!-- end of auto-generated comment: release notes by coderabbit.ai -->

   

   fgvieira authored Jun 11, 2025
   Configuration menu

   • View commit details
   • Copy full SHA for 965df4d
   • Browse repository at this point

   Copy the full SHA

   965df4d View commit details

   Browse the repository at this point in the history

4. feat: add param for mem_overhead (#4122) …

   <!-- Ensure that the PR title follows conventional commit style (<type>:
   <description>)-->
   <!-- Possible types are here:
   https://github.com/commitizen/conventional-commit-types/blob/master/index.json
   -->
   
   <!-- Add a description of your PR here-->
   
   ### QC
   <!-- Make sure that you can tick the boxes below. -->
   
   * [x] I confirm that I have followed the [documentation for contributing
   to
   `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).
   
   While the contributions guidelines are more extensive, please
   particularly ensure that:
   * [x] `test.py` was updated to call any added or updated example rules
   in a `Snakefile`
   * [x] `input:` and `output:` file paths in the rules can be chosen
   arbitrarily
   * [x] wherever possible, command line arguments are inferred and set
   automatically (e.g. based on file extensions in `input:` or `output:`)
   * [x] temporary files are either written to a unique hidden folder in
   the working directory, or (better) stored where the Python function
   `tempfile.gettempdir()` points to
   * [x] the `meta.yaml` contains a link to the documentation of the
   respective tool or command under `url:`
   * [x] conda environments use a minimal amount of channels and packages,
   in recommended ordering
   
   
   <!-- This is an auto-generated comment: release notes by coderabbit.ai
   -->
   ## Summary by CodeRabbit
   
   - **New Features**
   - Introduced a configurable memory overhead setting to optimize memory
   allocation during FastQC runs.
   - Enhanced output descriptions for FastQC results, clarifying file
   formats and contents.
   - **Refactor**
   - Improved memory management during FastQC execution to optimize
   resource allocation per thread, enhancing performance stability without
   changing user workflows.
   <!-- end of auto-generated comment: release notes by coderabbit.ai -->

   

   fgvieira authored Jun 11, 2025
   Configuration menu

   • View commit details
   • Copy full SHA for 50f8acb
   • Browse repository at this point

   Copy the full SHA

   50f8acb View commit details

   Browse the repository at this point in the history

5. chore(master): release 7.0.0 (#4124) …

   🤖 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).

   

   snakemake-bot authored Jun 11, 2025
   Configuration menu

   • View commit details
   • Copy full SHA for 516186d
   • Browse repository at this point

   Copy the full SHA

   516186d View commit details

   Browse the repository at this point in the history