Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: adds GRCm39 to default_effective_genome_size in deepTools bamCoverage #3164

Merged
merged 3 commits into from
Aug 31, 2024

Conversation

rtfcoimbra
Copy link
Contributor

@rtfcoimbra rtfcoimbra commented Aug 30, 2024

The deepTools documentation provides the effective genome size by read length for GRCm39, so I added it to the default_effective_genome_size dictionary in the deepTools bamCoverage wrapper. I've also made minor adjustments to the params in the "meta.yaml" file - i.e., added GRCm39 to genome, and 250 to read_length (which was already allowed in the code but missing from the docs).

QC

While the contributions guidelines are more extensive, please particularly ensure that:

  • test.py was updated to call any added or updated example rules in a Snakefile
  • input: and output: file paths in the rules can be chosen arbitrarily
  • 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
  • the meta.yaml contains a link to the documentation of the respective tool or command under url:
  • conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

  • New Features
    • Added support for the GRCm39 genome assembly in the configuration options.
    • Expanded the read_length parameter to include a new option of 250.

These updates enhance flexibility and functionality for users working with genomic data.

the `default_effective_genome_size` dict in `wrapper.py` includes the key-value pair `"250": <effective_genome_size>` for all available genomes, but it was missing from the params
Copy link
Contributor

coderabbitai bot commented Aug 30, 2024

Walkthrough

The changes involve updates to the bio/deeptools/bamcoverage configuration, specifically adding the genome assembly "GRCm39" and a new read length option of 250. The meta.yaml file now includes these options, while the wrapper.py file has been modified to accommodate the new genome assembly in its data structure. These updates expand the flexibility and functionality of the tool without altering existing capabilities.

Changes

Files Change Summary
bio/deeptools/bamcoverage/meta.yaml Added GRCm39 to the genome parameter and 250 to the read_length parameter.
bio/deeptools/bamcoverage/wrapper.py Introduced a new entry for "GRCm39" in the genome assembly data structure.

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share
Tips

Chat

There are 3 ways to chat with CodeRabbit:

  • Review comments: Directly reply to a review comment made by CodeRabbit. Example:
    • I pushed a fix in commit <commit_id>.
    • Generate unit testing code for this file.
    • Open a follow-up GitHub issue for this discussion.
  • Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
    • @coderabbitai generate unit testing code for this file.
    • @coderabbitai modularize this function.
  • PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
    • @coderabbitai generate interesting stats about this repository and render them as a table.
    • @coderabbitai show all the console.log statements in this repository.
    • @coderabbitai read src/utils.ts and generate unit testing code.
    • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
    • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

  • @coderabbitai pause to pause the reviews on a PR.
  • @coderabbitai resume to resume the paused reviews.
  • @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
  • @coderabbitai full review to do a full review from scratch and review all the files again.
  • @coderabbitai summary to regenerate the summary of the PR.
  • @coderabbitai resolve resolve all the CodeRabbit review comments.
  • @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
  • @coderabbitai help to get help.

Other keywords and placeholders

  • Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
  • Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
  • Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

  • You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
  • Please see the configuration documentation for more information.
  • If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

  • Visit our Documentation for detailed information on how to use CodeRabbit.
  • Join our Discord Community to get help, request features, and share feedback.
  • Follow us on X/Twitter for updates and announcements.

Copy link
Contributor

@coderabbitai coderabbitai bot left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between bb4acf9 and 8401125.

Files selected for processing (2)
  • bio/deeptools/bamcoverage/meta.yaml (1 hunks)
  • bio/deeptools/bamcoverage/wrapper.py (1 hunks)
Additional context used
Path-based instructions (1)
bio/deeptools/bamcoverage/wrapper.py (2)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.


Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

Additional comments not posted (3)
bio/deeptools/bamcoverage/meta.yaml (2)

15-15: Addition of GRCm39 to genome options.

The inclusion of GRCm39 alongside other genome versions like GRCm37 and GRCm38 is consistent and expands the tool's applicability to newer genome assemblies.

The code changes are approved.


16-16: Expansion of read length options to include 250.

Adding 250 to the read_length options aligns with the PR's objective to reflect the existing code capabilities in the documentation, enhancing user flexibility in specifying read lengths.

The code changes are approved.

bio/deeptools/bamcoverage/wrapper.py (1)

45-51: Addition of GRCm39 to effective genome size mapping.

The inclusion of GRCm39 with specific values for different read lengths (50, 75, 100, 150, 200, 250) is consistent with the structure used for other genome assemblies. This addition enhances the tool's functionality by supporting a newer genome assembly.

The code changes are approved.

@fgvieira fgvieira enabled auto-merge (squash) August 31, 2024 12:40
@fgvieira fgvieira merged commit b5916c4 into snakemake:master Aug 31, 2024
7 checks passed
fgvieira pushed a commit that referenced this pull request Sep 17, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[4.4.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.3.0...v4.4.0)
(2024-09-17)


### Features

* adds GRCm39 to `default_effective_genome_size` in deepTools
bamCoverage
([#3164](https://www.github.com/snakemake/snakemake-wrappers/issues/3164))
([b5916c4](https://www.github.com/snakemake/snakemake-wrappers/commit/b5916c4bff9e3ab009bf57ff66873770b344cf0d))
* Bwameth index
([#3162](https://www.github.com/snakemake/snakemake-wrappers/issues/3162))
([bb4acf9](https://www.github.com/snakemake/snakemake-wrappers/commit/bb4acf978165278a1dac14b86c98ffecd1534b29))


### Performance Improvements

* autobump bio/adapterremoval
([#3144](https://www.github.com/snakemake/snakemake-wrappers/issues/3144))
([ddebbec](https://www.github.com/snakemake/snakemake-wrappers/commit/ddebbece33b3e7d95abed984ac7ceb6277209379))
* autobump bio/bcftools/call
([#3188](https://www.github.com/snakemake/snakemake-wrappers/issues/3188))
([482a506](https://www.github.com/snakemake/snakemake-wrappers/commit/482a5060b1fac0db9eb909c9b1838876a00ca9a9))
* autobump bio/bcftools/concat
([#3172](https://www.github.com/snakemake/snakemake-wrappers/issues/3172))
([25e18b3](https://www.github.com/snakemake/snakemake-wrappers/commit/25e18b3d16bd324068ce25100da25dce29616002))
* autobump bio/bcftools/filter
([#3187](https://www.github.com/snakemake/snakemake-wrappers/issues/3187))
([2872f7b](https://www.github.com/snakemake/snakemake-wrappers/commit/2872f7b2eb43bcdd16f2ef2e8ebf600c3cd3b1aa))
* autobump bio/bcftools/index
([#3202](https://www.github.com/snakemake/snakemake-wrappers/issues/3202))
([8e7f67c](https://www.github.com/snakemake/snakemake-wrappers/commit/8e7f67cd2b91246662b4fd8b9208661624fdfa9c))
* autobump bio/bcftools/merge
([#3194](https://www.github.com/snakemake/snakemake-wrappers/issues/3194))
([e5e3aea](https://www.github.com/snakemake/snakemake-wrappers/commit/e5e3aeaf4c4345464bf353825dd69d11d9355a40))
* autobump bio/bcftools/mpileup
([#3195](https://www.github.com/snakemake/snakemake-wrappers/issues/3195))
([abddbbe](https://www.github.com/snakemake/snakemake-wrappers/commit/abddbbe42f34da7ce6d34c65c17cd0b4aad2b2b3))
* autobump bio/bcftools/norm
([#3176](https://www.github.com/snakemake/snakemake-wrappers/issues/3176))
([44ee589](https://www.github.com/snakemake/snakemake-wrappers/commit/44ee589ddcdc2c94bc7f155d43f12688f288ccef))
* autobump bio/bcftools/reheader
([#3191](https://www.github.com/snakemake/snakemake-wrappers/issues/3191))
([ce681c6](https://www.github.com/snakemake/snakemake-wrappers/commit/ce681c6e8078beef7767c9f18156f573ecc80396))
* autobump bio/bcftools/sort
([#3192](https://www.github.com/snakemake/snakemake-wrappers/issues/3192))
([1333676](https://www.github.com/snakemake/snakemake-wrappers/commit/1333676d6aa0e573c46635e9e0e958e1d42bf671))
* autobump bio/bcftools/stats
([#3193](https://www.github.com/snakemake/snakemake-wrappers/issues/3193))
([aeadc98](https://www.github.com/snakemake/snakemake-wrappers/commit/aeadc98f39aa1c4806f81e694a8ef865cca6dab1))
* autobump bio/bcftools/view
([#3183](https://www.github.com/snakemake/snakemake-wrappers/issues/3183))
([52ecefe](https://www.github.com/snakemake/snakemake-wrappers/commit/52ecefe6da982aa9f20b1e507e5a177a77c59c2e))
* autobump bio/bellerophon
([#3184](https://www.github.com/snakemake/snakemake-wrappers/issues/3184))
([c123ef8](https://www.github.com/snakemake/snakemake-wrappers/commit/c123ef803c0737f6f0a9f20d8496ce5bf6c6f8ac))
* autobump bio/benchmark/chm-eval-sample
([#3201](https://www.github.com/snakemake/snakemake-wrappers/issues/3201))
([95fb4d7](https://www.github.com/snakemake/snakemake-wrappers/commit/95fb4d78fa280e363478535bf7f118f88ed96905))
* autobump bio/bgzip
([#3198](https://www.github.com/snakemake/snakemake-wrappers/issues/3198))
([344637b](https://www.github.com/snakemake/snakemake-wrappers/commit/344637b6aafb7e2ea619786a82c4779755150237))
* autobump bio/bismark/bam2nuc
([#3173](https://www.github.com/snakemake/snakemake-wrappers/issues/3173))
([e076c15](https://www.github.com/snakemake/snakemake-wrappers/commit/e076c15b77e6e09d8c4998ee5501c13557d7001a))
* autobump bio/bismark/bismark
([#3190](https://www.github.com/snakemake/snakemake-wrappers/issues/3190))
([43650cb](https://www.github.com/snakemake/snakemake-wrappers/commit/43650cb23abc76b01116b4e07e5362d113d0d168))
* autobump bio/bismark/bismark_genome_preparation
([#3178](https://www.github.com/snakemake/snakemake-wrappers/issues/3178))
([1f05814](https://www.github.com/snakemake/snakemake-wrappers/commit/1f058140265c60c6b4752d5644879e7b57ec0cdd))
* autobump bio/bismark/bismark_methylation_extractor
([#3177](https://www.github.com/snakemake/snakemake-wrappers/issues/3177))
([b9fb8a1](https://www.github.com/snakemake/snakemake-wrappers/commit/b9fb8a1f8f3636740cf0e9dc5893732d45a5a120))
* autobump bio/bismark/bismark2bedGraph
([#3179](https://www.github.com/snakemake/snakemake-wrappers/issues/3179))
([e43eca7](https://www.github.com/snakemake/snakemake-wrappers/commit/e43eca70a859687cda1696f4f5c54137c064e349))
* autobump bio/bismark/bismark2report
([#3174](https://www.github.com/snakemake/snakemake-wrappers/issues/3174))
([0697536](https://www.github.com/snakemake/snakemake-wrappers/commit/0697536319d030fa281ce6d9682ed2c4c4fdf197))
* autobump bio/bismark/bismark2summary
([#3197](https://www.github.com/snakemake/snakemake-wrappers/issues/3197))
([1684162](https://www.github.com/snakemake/snakemake-wrappers/commit/168416226f05b0a202a8b2dd7b3c038a5abe1fe7))
* autobump bio/bismark/deduplicate_bismark
([#3196](https://www.github.com/snakemake/snakemake-wrappers/issues/3196))
([f864fde](https://www.github.com/snakemake/snakemake-wrappers/commit/f864fded50ae5f79ee9c2af08732dd43efa8f1ee))
* autobump bio/bowtie2/align
([#3199](https://www.github.com/snakemake/snakemake-wrappers/issues/3199))
([38e12a9](https://www.github.com/snakemake/snakemake-wrappers/commit/38e12a95a9091921c2edb7d62b8591049362ac02))
* autobump bio/bustools/count
([#3189](https://www.github.com/snakemake/snakemake-wrappers/issues/3189))
([16144ab](https://www.github.com/snakemake/snakemake-wrappers/commit/16144abda060631368c2aabef253cd4884dbbe8e))
* autobump bio/bustools/sort
([#3175](https://www.github.com/snakemake/snakemake-wrappers/issues/3175))
([be5264b](https://www.github.com/snakemake/snakemake-wrappers/commit/be5264bf8204bde79525d96a69fb930d3832c643))
* autobump bio/bustools/text
([#3185](https://www.github.com/snakemake/snakemake-wrappers/issues/3185))
([6457e25](https://www.github.com/snakemake/snakemake-wrappers/commit/6457e257d11ec13faa6bd5f0f5ea15640051736a))
* autobump bio/bwa-mem2/mem
([#3180](https://www.github.com/snakemake/snakemake-wrappers/issues/3180))
([72d688b](https://www.github.com/snakemake/snakemake-wrappers/commit/72d688b328f6e98e41e333ae61fcf9d452cb7bd9))
* autobump bio/bwa-meme/mem
([#3182](https://www.github.com/snakemake/snakemake-wrappers/issues/3182))
([c0f3f1b](https://www.github.com/snakemake/snakemake-wrappers/commit/c0f3f1b07900ed88a88a09c6699d1f58322e91c0))
* autobump bio/bwa-memx/mem
([#3181](https://www.github.com/snakemake/snakemake-wrappers/issues/3181))
([aeae606](https://www.github.com/snakemake/snakemake-wrappers/commit/aeae606ae4d23c939fad62bf0c10c31e3758a035))
* autobump bio/bwa/mem
([#3204](https://www.github.com/snakemake/snakemake-wrappers/issues/3204))
([9faa47f](https://www.github.com/snakemake/snakemake-wrappers/commit/9faa47fb057ad09cbd485e6188d9738c8e1d0b9f))
* autobump bio/bwa/sampe
([#3200](https://www.github.com/snakemake/snakemake-wrappers/issues/3200))
([4b09e72](https://www.github.com/snakemake/snakemake-wrappers/commit/4b09e72674c9d5097524faa9d794fbd02706cae0))
* autobump bio/bwa/samse
([#3203](https://www.github.com/snakemake/snakemake-wrappers/issues/3203))
([e5242a6](https://www.github.com/snakemake/snakemake-wrappers/commit/e5242a6813da87a49f7ab3f1dffd4a0e5d6b7dd9))
* autobump bio/bwa/samxe
([#3186](https://www.github.com/snakemake/snakemake-wrappers/issues/3186))
([5e4a55a](https://www.github.com/snakemake/snakemake-wrappers/commit/5e4a55ac95fd79afc3dc7713d74cfabed0e0d4f7))
* autobump bio/cnvkit/export
([#3205](https://www.github.com/snakemake/snakemake-wrappers/issues/3205))
([7b139c1](https://www.github.com/snakemake/snakemake-wrappers/commit/7b139c1fc73073ad5f2ccaf182caf099fe85b4fb))
* autobump bio/emu/abundance
([#3147](https://www.github.com/snakemake/snakemake-wrappers/issues/3147))
([a7cad86](https://www.github.com/snakemake/snakemake-wrappers/commit/a7cad866cae928ce465c96345eab4845e36d23f6))
* autobump bio/emu/collapse-taxonomy
([#3148](https://www.github.com/snakemake/snakemake-wrappers/issues/3148))
([0edc83d](https://www.github.com/snakemake/snakemake-wrappers/commit/0edc83d7220f52bcb677024d443ba3e39baddf45))
* autobump bio/emu/combine-outputs
([#3146](https://www.github.com/snakemake/snakemake-wrappers/issues/3146))
([93f0557](https://www.github.com/snakemake/snakemake-wrappers/commit/93f0557bde9524f93d0663a05eae11bb0c43d3fd))
* autobump bio/freebayes
([#3168](https://www.github.com/snakemake/snakemake-wrappers/issues/3168))
([57c126d](https://www.github.com/snakemake/snakemake-wrappers/commit/57c126d7df1a163f593d3fccca50c7c0143a1fd2))
* autobump bio/freebayes
([#3206](https://www.github.com/snakemake/snakemake-wrappers/issues/3206))
([3a04dc4](https://www.github.com/snakemake/snakemake-wrappers/commit/3a04dc4ba9ae4506b97aa0e2d732d3896e1a0f2f))
* autobump bio/gatk/applybqsr
([#3207](https://www.github.com/snakemake/snakemake-wrappers/issues/3207))
([8b0fe36](https://www.github.com/snakemake/snakemake-wrappers/commit/8b0fe36569bb2d0ec225e6aaf9a2078b195301a4))
* autobump bio/gatk/applybqsrspark
([#3208](https://www.github.com/snakemake/snakemake-wrappers/issues/3208))
([f51e681](https://www.github.com/snakemake/snakemake-wrappers/commit/f51e6815d9774a8bd50f1a56d6a5ca33bf00b2ab))
* autobump bio/hisat2/align
([#3209](https://www.github.com/snakemake/snakemake-wrappers/issues/3209))
([8eeba48](https://www.github.com/snakemake/snakemake-wrappers/commit/8eeba482eecca72a8fc244f6cdeeb43bfae2d3a5))
* autobump bio/hisat2/index
([#3210](https://www.github.com/snakemake/snakemake-wrappers/issues/3210))
([9a67a1b](https://www.github.com/snakemake/snakemake-wrappers/commit/9a67a1b244f07e79addce42d31bea0dcffa0413e))
* autobump bio/homer/makeTagDirectory
([#3211](https://www.github.com/snakemake/snakemake-wrappers/issues/3211))
([6d22fe9](https://www.github.com/snakemake/snakemake-wrappers/commit/6d22fe95fd05930210a6e15c39921a2dac287c66))
* autobump bio/last/lastal
([#3149](https://www.github.com/snakemake/snakemake-wrappers/issues/3149))
([9bba079](https://www.github.com/snakemake/snakemake-wrappers/commit/9bba0798f68f2060116d8b27b7f9bd5f659655db))
* autobump bio/last/lastal
([#3169](https://www.github.com/snakemake/snakemake-wrappers/issues/3169))
([c119c2f](https://www.github.com/snakemake/snakemake-wrappers/commit/c119c2f49e3c803db3158bf0f661fba93fa06424))
* autobump bio/last/lastdb
([#3150](https://www.github.com/snakemake/snakemake-wrappers/issues/3150))
([ecdd8b4](https://www.github.com/snakemake/snakemake-wrappers/commit/ecdd8b4fc48ac69b66474afe96e04f254a7dac67))
* autobump bio/last/lastdb
([#3170](https://www.github.com/snakemake/snakemake-wrappers/issues/3170))
([5928b90](https://www.github.com/snakemake/snakemake-wrappers/commit/5928b90d882ce13468414cd58989c3624a03e43e))
* autobump bio/minimap2/aligner
([#3212](https://www.github.com/snakemake/snakemake-wrappers/issues/3212))
([b6b8881](https://www.github.com/snakemake/snakemake-wrappers/commit/b6b888141c3a9813ec54ef40bb231e9beeba8c37))
* autobump bio/open-cravat/module
([#3152](https://www.github.com/snakemake/snakemake-wrappers/issues/3152))
([0ad5486](https://www.github.com/snakemake/snakemake-wrappers/commit/0ad5486dd375a1d418934a71f8a0153519ecf959))
* autobump bio/open-cravat/run
([#3151](https://www.github.com/snakemake/snakemake-wrappers/issues/3151))
([1b1be2e](https://www.github.com/snakemake/snakemake-wrappers/commit/1b1be2eff54cb9542d425b44afe16f930f5aab1e))
* autobump bio/paladin/align
([#3217](https://www.github.com/snakemake/snakemake-wrappers/issues/3217))
([9d48a9b](https://www.github.com/snakemake/snakemake-wrappers/commit/9d48a9b0f318b3f80aafbb79593e7657325db3cf))
* autobump bio/paladin/index
([#3213](https://www.github.com/snakemake/snakemake-wrappers/issues/3213))
([9107d7d](https://www.github.com/snakemake/snakemake-wrappers/commit/9107d7d4ee1658330c50c501cab14bc9c23b0bba))
* autobump bio/paladin/prepare
([#3216](https://www.github.com/snakemake/snakemake-wrappers/issues/3216))
([5420331](https://www.github.com/snakemake/snakemake-wrappers/commit/54203311f914e2ef77e89c0341a77ad068b07e41))
* autobump bio/pcaexplorer/pcaplot
([#3153](https://www.github.com/snakemake/snakemake-wrappers/issues/3153))
([7adabb5](https://www.github.com/snakemake/snakemake-wrappers/commit/7adabb520ae851041bf50cefe9293dab22799b26))
* autobump bio/picard/markduplicates
([#3214](https://www.github.com/snakemake/snakemake-wrappers/issues/3214))
([902ac1f](https://www.github.com/snakemake/snakemake-wrappers/commit/902ac1ff96405b16f1c2c6c927e38afcb236219b))
* autobump bio/pretext/map
([#3215](https://www.github.com/snakemake/snakemake-wrappers/issues/3215))
([e77b8a9](https://www.github.com/snakemake/snakemake-wrappers/commit/e77b8a9bda9970e7209507eab2df4e48253c6d29))
* autobump bio/rasusa
([#3155](https://www.github.com/snakemake/snakemake-wrappers/issues/3155))
([44f944f](https://www.github.com/snakemake/snakemake-wrappers/commit/44f944f39f6f922b6255093c1b69a7fa3b7ddc8e))
* autobump bio/reference/ensembl-variation
([#3218](https://www.github.com/snakemake/snakemake-wrappers/issues/3218))
([5da1b1d](https://www.github.com/snakemake/snakemake-wrappers/commit/5da1b1d7ae4d86e29603811d385df006dc934438))
* autobump bio/rseqc/bam_stat
([#3154](https://www.github.com/snakemake/snakemake-wrappers/issues/3154))
([a5f16b3](https://www.github.com/snakemake/snakemake-wrappers/commit/a5f16b357c04e8457d2175baed3a60ee5314db73))
* autobump bio/samtools/calmd
([#3239](https://www.github.com/snakemake/snakemake-wrappers/issues/3239))
([91cf673](https://www.github.com/snakemake/snakemake-wrappers/commit/91cf6736736613254b3fbc157cdc6aed06eedfd9))
* autobump bio/samtools/collate
([#3229](https://www.github.com/snakemake/snakemake-wrappers/issues/3229))
([4e062a1](https://www.github.com/snakemake/snakemake-wrappers/commit/4e062a14219cb3dafdfea1330f197298d72f9b1a))
* autobump bio/samtools/depth
([#3225](https://www.github.com/snakemake/snakemake-wrappers/issues/3225))
([35321e4](https://www.github.com/snakemake/snakemake-wrappers/commit/35321e4408b6681bb34648a3fa0110c2848479e2))
* autobump bio/samtools/faidx
([#3223](https://www.github.com/snakemake/snakemake-wrappers/issues/3223))
([dd5bdc9](https://www.github.com/snakemake/snakemake-wrappers/commit/dd5bdc9ab84cca52c6f22745c9de476572ec1297))
* autobump bio/samtools/fastx
([#3220](https://www.github.com/snakemake/snakemake-wrappers/issues/3220))
([aa8147e](https://www.github.com/snakemake/snakemake-wrappers/commit/aa8147e4c2bd6d13499e427a8f0d27369754f7e4))
* autobump bio/samtools/fixmate
([#3237](https://www.github.com/snakemake/snakemake-wrappers/issues/3237))
([54512e3](https://www.github.com/snakemake/snakemake-wrappers/commit/54512e3f540fcdc6f1ad636ddbe5fbb048075416))
* autobump bio/samtools/flagstat
([#3224](https://www.github.com/snakemake/snakemake-wrappers/issues/3224))
([5807a59](https://www.github.com/snakemake/snakemake-wrappers/commit/5807a59eb723285aa3ea6d431b455a443f06bf0b))
* autobump bio/samtools/idxstats
([#3231](https://www.github.com/snakemake/snakemake-wrappers/issues/3231))
([179dcd7](https://www.github.com/snakemake/snakemake-wrappers/commit/179dcd73c5442b8a10935061afce7240b778e6ed))
* autobump bio/samtools/index
([#3221](https://www.github.com/snakemake/snakemake-wrappers/issues/3221))
([375cfb6](https://www.github.com/snakemake/snakemake-wrappers/commit/375cfb65f6d1abf8d1bca744bc14ec5b1412e4b2))
* autobump bio/samtools/markdup
([#3219](https://www.github.com/snakemake/snakemake-wrappers/issues/3219))
([f01ce20](https://www.github.com/snakemake/snakemake-wrappers/commit/f01ce2063e2c22e99858c035666a6bb4e549a20b))
* autobump bio/samtools/merge
([#3236](https://www.github.com/snakemake/snakemake-wrappers/issues/3236))
([ea84b58](https://www.github.com/snakemake/snakemake-wrappers/commit/ea84b5894d27f9da2d0e9a5d07b014b5d98733c3))
* autobump bio/samtools/mpileup
([#3222](https://www.github.com/snakemake/snakemake-wrappers/issues/3222))
([728a8c5](https://www.github.com/snakemake/snakemake-wrappers/commit/728a8c53a8fd7de8831da13a93638a7cda073443))
* autobump bio/samtools/sort
([#3230](https://www.github.com/snakemake/snakemake-wrappers/issues/3230))
([65f98d3](https://www.github.com/snakemake/snakemake-wrappers/commit/65f98d377b954b828c2081c8019f04a335d27f13))
* autobump bio/samtools/stats
([#3238](https://www.github.com/snakemake/snakemake-wrappers/issues/3238))
([da97159](https://www.github.com/snakemake/snakemake-wrappers/commit/da97159e3523590c3a1a57f1d7dcdc3e4d0597f5))
* autobump bio/samtools/view
([#3233](https://www.github.com/snakemake/snakemake-wrappers/issues/3233))
([69514b5](https://www.github.com/snakemake/snakemake-wrappers/commit/69514b5966155d32b0a199efc3647449613b2136))
* autobump bio/snpeff/annotate
([#3226](https://www.github.com/snakemake/snakemake-wrappers/issues/3226))
([01a432e](https://www.github.com/snakemake/snakemake-wrappers/commit/01a432ed553a2a1d1ae783f9170d331e28616a83))
* autobump bio/snpeff/download
([#3228](https://www.github.com/snakemake/snakemake-wrappers/issues/3228))
([58c57ca](https://www.github.com/snakemake/snakemake-wrappers/commit/58c57caf6799c4585dd45ff02906d3e71f487b40))
* autobump bio/snpsift/annotate
([#3232](https://www.github.com/snakemake/snakemake-wrappers/issues/3232))
([f5697bb](https://www.github.com/snakemake/snakemake-wrappers/commit/f5697bbb43b9fa6c1d1597ee77dddd0c70be842f))
* autobump bio/snpsift/dbnsfp
([#3227](https://www.github.com/snakemake/snakemake-wrappers/issues/3227))
([c4ffeca](https://www.github.com/snakemake/snakemake-wrappers/commit/c4ffeca7b5709f356446777d05ee4781bf53d091))
* autobump bio/snpsift/genesets
([#3234](https://www.github.com/snakemake/snakemake-wrappers/issues/3234))
([fd68948](https://www.github.com/snakemake/snakemake-wrappers/commit/fd6894828e567bb8dc180331b77560380a4b688d))
* autobump bio/snpsift/gwascat
([#3235](https://www.github.com/snakemake/snakemake-wrappers/issues/3235))
([1f4a77d](https://www.github.com/snakemake/snakemake-wrappers/commit/1f4a77d86e671d36d064113a82af6d2bbfc08451))
* autobump bio/ucsc/bedGraphToBigWig
([#3160](https://www.github.com/snakemake/snakemake-wrappers/issues/3160))
([a8c4f3b](https://www.github.com/snakemake/snakemake-wrappers/commit/a8c4f3bc9183e161ed1721a520471fd72bc16d2b))
* autobump bio/ucsc/faToTwoBit
([#3156](https://www.github.com/snakemake/snakemake-wrappers/issues/3156))
([5745452](https://www.github.com/snakemake/snakemake-wrappers/commit/5745452ca8ef5567b8df2f6187836d47a29925d9))
* autobump bio/ucsc/genePredToBed
([#3158](https://www.github.com/snakemake/snakemake-wrappers/issues/3158))
([8f1db22](https://www.github.com/snakemake/snakemake-wrappers/commit/8f1db225877c81932da88893624a4dcc60e052ee))
* autobump bio/ucsc/gtfToGenePred
([#3159](https://www.github.com/snakemake/snakemake-wrappers/issues/3159))
([6faa0c6](https://www.github.com/snakemake/snakemake-wrappers/commit/6faa0c6fb9d21a62d17fc773e213bc857c83c139))
* autobump bio/ucsc/twoBitInfo
([#3157](https://www.github.com/snakemake/snakemake-wrappers/issues/3157))
([40175c0](https://www.github.com/snakemake/snakemake-wrappers/commit/40175c0ad4c0e3a0b0f3fca8bfe824b3989844de))
* autobump bio/ucsc/twoBitToFa
([#3161](https://www.github.com/snakemake/snakemake-wrappers/issues/3161))
([f79e634](https://www.github.com/snakemake/snakemake-wrappers/commit/f79e634602ab849221219a9928d9d80e9aa9d31e))
* autobump bio/umis/bamtag
([#3241](https://www.github.com/snakemake/snakemake-wrappers/issues/3241))
([c56de46](https://www.github.com/snakemake/snakemake-wrappers/commit/c56de46f89a475e0e37629e25e235deda6a347d8))
* autobump bio/unicycler
([#3240](https://www.github.com/snakemake/snakemake-wrappers/issues/3240))
([7636292](https://www.github.com/snakemake/snakemake-wrappers/commit/763629260216e75a13b64e10da15e94b2fcd780a))
* autobump bio/vg/construct
([#3244](https://www.github.com/snakemake/snakemake-wrappers/issues/3244))
([276ff3d](https://www.github.com/snakemake/snakemake-wrappers/commit/276ff3d272ddbfb3a8a14d31300d24511d6e369b))
* autobump bio/vg/ids
([#3242](https://www.github.com/snakemake/snakemake-wrappers/issues/3242))
([105e474](https://www.github.com/snakemake/snakemake-wrappers/commit/105e474d60b98787ad49b5f3720a7256e8bac07a))
* autobump bio/vg/kmers
([#3245](https://www.github.com/snakemake/snakemake-wrappers/issues/3245))
([ffab8f4](https://www.github.com/snakemake/snakemake-wrappers/commit/ffab8f466a9aef907ad51344326b2de0f5a8f40e))
* autobump bio/vg/merge
([#3247](https://www.github.com/snakemake/snakemake-wrappers/issues/3247))
([20defe3](https://www.github.com/snakemake/snakemake-wrappers/commit/20defe34945248316d7fb0dae58f40d9531835c0))
* autobump bio/vg/prune
([#3243](https://www.github.com/snakemake/snakemake-wrappers/issues/3243))
([60a29bf](https://www.github.com/snakemake/snakemake-wrappers/commit/60a29bf1f76b6dadaf3a9636eca9d9cc5a44dd68))
* autobump bio/vg/sim
([#3246](https://www.github.com/snakemake/snakemake-wrappers/issues/3246))
([b687ab2](https://www.github.com/snakemake/snakemake-wrappers/commit/b687ab2debfd2e7565541b2643b1f44556ee2489))
* autobump utils/datavzrd
([#3167](https://www.github.com/snakemake/snakemake-wrappers/issues/3167))
([35fa029](https://www.github.com/snakemake/snakemake-wrappers/commit/35fa0297bea8b1f357542c272a383080a0f1895a))
* Update datavzrd wrapper
([#3166](https://www.github.com/snakemake/snakemake-wrappers/issues/3166))
([7d3aa9d](https://www.github.com/snakemake/snakemake-wrappers/commit/7d3aa9da588e97a548b0904366a4ab47941cb73c))
* Update utils/datavzrd
([#3248](https://www.github.com/snakemake/snakemake-wrappers/issues/3248))
([12076f6](https://www.github.com/snakemake/snakemake-wrappers/commit/12076f630d3a4764e5b4756951c642a35c9bb0f4))
---


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

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants