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feat: Add support for regions file and arbitrary FAI/GZI paths #2936

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merged 5 commits into from
May 20, 2024

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fgvieira
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QC

  • I confirm that:

For all wrappers added by this PR,

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • 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 (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.
  • Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

@fgvieira fgvieira merged commit 445b35f into snakemake:master May 20, 2024
6 checks passed
@fgvieira fgvieira deleted the samtools_faidx branch May 21, 2024 08:38
fgvieira pushed a commit that referenced this pull request Jun 3, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.11.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.2...v3.11.0)
(2024-05-31)


### Features

* add samtools markdup wrapper
([#2926](https://www.github.com/snakemake/snakemake-wrappers/issues/2926))
([3c86bae](https://www.github.com/snakemake/snakemake-wrappers/commit/3c86baef4586b596c6c3375336828257e8bb815f))
* Add support for regions file and arbitrary FAI/GZI paths
([#2936](https://www.github.com/snakemake/snakemake-wrappers/issues/2936))
([445b35f](https://www.github.com/snakemake/snakemake-wrappers/commit/445b35f314f035d8248ca84cb16b273b0e65847c))
* add wrapper to samtools collate
([#2929](https://www.github.com/snakemake/snakemake-wrappers/issues/2929))
([0c7ae27](https://www.github.com/snakemake/snakemake-wrappers/commit/0c7ae27622e45167b9cc1aaf1be238b0d25429b9))
* All ngsderive subcommands
([#2732](https://www.github.com/snakemake/snakemake-wrappers/issues/2732))
([847ab1d](https://www.github.com/snakemake/snakemake-wrappers/commit/847ab1d918c09908bcdb40fa3413b6dbc88d4803))
* auto infer run mode
([#2937](https://www.github.com/snakemake/snakemake-wrappers/issues/2937))
([08bd3cd](https://www.github.com/snakemake/snakemake-wrappers/commit/08bd3cd79243c4c0636f88d229667e58595611bd))
* Goleft indexcov
([#2734](https://www.github.com/snakemake/snakemake-wrappers/issues/2734))
([ebef6f8](https://www.github.com/snakemake/snakemake-wrappers/commit/ebef6f8259e89d9a06b2264a5d0a34da23d2e84e))


### Bug Fixes

* bamcoverage without effective genome size
([#2941](https://www.github.com/snakemake/snakemake-wrappers/issues/2941))
([b6ad55f](https://www.github.com/snakemake/snakemake-wrappers/commit/b6ad55f4d2c702ecc904d6b40b4b35b2463c895a))
* issue
[#366](https://www.github.com/snakemake/snakemake-wrappers/issues/366)
and
[#2649](https://www.github.com/snakemake/snakemake-wrappers/issues/2649)
([#2928](https://www.github.com/snakemake/snakemake-wrappers/issues/2928))
([e10ab57](https://www.github.com/snakemake/snakemake-wrappers/commit/e10ab571a63b36ce1295e50b6f6b7e4742e0beae))
* remove NA string replacement, fixed upstream
([#2940](https://www.github.com/snakemake/snakemake-wrappers/issues/2940))
([8f4d223](https://www.github.com/snakemake/snakemake-wrappers/commit/8f4d223ec6c1e1e2715708d0532399ede4ed2727))


### Performance Improvements

* autobump bio/bismark/bam2nuc
([#2943](https://www.github.com/snakemake/snakemake-wrappers/issues/2943))
([9228479](https://www.github.com/snakemake/snakemake-wrappers/commit/9228479896c2410ae6a58849bf59e5f01bc5e712))
* autobump bio/bismark/bismark
([#2948](https://www.github.com/snakemake/snakemake-wrappers/issues/2948))
([d9abb20](https://www.github.com/snakemake/snakemake-wrappers/commit/d9abb20e0e002d9ec16507d86211b0555a2546ba))
* autobump bio/bismark/bismark_genome_preparation
([#2945](https://www.github.com/snakemake/snakemake-wrappers/issues/2945))
([899ae0d](https://www.github.com/snakemake/snakemake-wrappers/commit/899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6))
* autobump bio/bismark/bismark_methylation_extractor
([#2944](https://www.github.com/snakemake/snakemake-wrappers/issues/2944))
([1b232d2](https://www.github.com/snakemake/snakemake-wrappers/commit/1b232d24816a40f75568bec224eff4e164b3f953))
* autobump bio/bismark/bismark2bedGraph
([#2947](https://www.github.com/snakemake/snakemake-wrappers/issues/2947))
([ab29098](https://www.github.com/snakemake/snakemake-wrappers/commit/ab29098757c3eef17884f198234ec456e19414f9))
* autobump bio/bismark/bismark2report
([#2951](https://www.github.com/snakemake/snakemake-wrappers/issues/2951))
([13dd155](https://www.github.com/snakemake/snakemake-wrappers/commit/13dd155a20025b8aaaa80ce3747e6822562bb6b1))
* autobump bio/bismark/bismark2summary
([#2946](https://www.github.com/snakemake/snakemake-wrappers/issues/2946))
([bfb3d30](https://www.github.com/snakemake/snakemake-wrappers/commit/bfb3d305daa519faee4ad4ea7dbd313941f4c128))
* autobump bio/bismark/deduplicate_bismark
([#2950](https://www.github.com/snakemake/snakemake-wrappers/issues/2950))
([bcf3c06](https://www.github.com/snakemake/snakemake-wrappers/commit/bcf3c06887443dae9749254f0e8d34e30f880b7e))
* autobump bio/bowtie2/align
([#2949](https://www.github.com/snakemake/snakemake-wrappers/issues/2949))
([6b0593f](https://www.github.com/snakemake/snakemake-wrappers/commit/6b0593facfcae0b9c92cb1f31423426752c0230d))
* autobump bio/bowtie2/build
([#2942](https://www.github.com/snakemake/snakemake-wrappers/issues/2942))
([5b3ca20](https://www.github.com/snakemake/snakemake-wrappers/commit/5b3ca20635bd0e427a548e68cd8a40fdb0047f10))
* autobump bio/bwa-mem2/mem-samblaster
([#2962](https://www.github.com/snakemake/snakemake-wrappers/issues/2962))
([ff613f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ff613f37f857f23d19e4dc0cace22b02113a7e07))
* autobump bio/bwa/mem-samblaster
([#2961](https://www.github.com/snakemake/snakemake-wrappers/issues/2961))
([83754dd](https://www.github.com/snakemake/snakemake-wrappers/commit/83754dd9f158ea978faa1ed33668a6dda648cdb7))
* autobump bio/fastq_screen
([#2952](https://www.github.com/snakemake/snakemake-wrappers/issues/2952))
([e45fcac](https://www.github.com/snakemake/snakemake-wrappers/commit/e45fcac221ef45f345a516bff905a53c864e7355))
* autobump bio/freebayes
([#2963](https://www.github.com/snakemake/snakemake-wrappers/issues/2963))
([7a0d553](https://www.github.com/snakemake/snakemake-wrappers/commit/7a0d553e09921cebc77b54d314c211b91099f7bd))
* autobump bio/gatk/applybqsr
([#2938](https://www.github.com/snakemake/snakemake-wrappers/issues/2938))
([498c67f](https://www.github.com/snakemake/snakemake-wrappers/commit/498c67fb12691b0021a7b234dfc279957b46708c))
* autobump bio/gatk3/realignertargetcreator
([#2931](https://www.github.com/snakemake/snakemake-wrappers/issues/2931))
([2d2835c](https://www.github.com/snakemake/snakemake-wrappers/commit/2d2835c51f974f7f45420f832b8084520d2d3ec0))
* autobump bio/gdc-api/bam-slicing
([#2954](https://www.github.com/snakemake/snakemake-wrappers/issues/2954))
([32d25c1](https://www.github.com/snakemake/snakemake-wrappers/commit/32d25c1560b4c581694c49dc6d3a596e5ca581ab))
* autobump bio/goleft/indexcov
([#2930](https://www.github.com/snakemake/snakemake-wrappers/issues/2930))
([5ccbdb0](https://www.github.com/snakemake/snakemake-wrappers/commit/5ccbdb078a835ad0c2fd3e9e63677103fe216eeb))
* autobump bio/gseapy/gsea
([#2953](https://www.github.com/snakemake/snakemake-wrappers/issues/2953))
([dda3d16](https://www.github.com/snakemake/snakemake-wrappers/commit/dda3d16c9b49145bd58d287db1021c41d5a24710))
* autobump bio/hifiasm
([#2932](https://www.github.com/snakemake/snakemake-wrappers/issues/2932))
([3722de7](https://www.github.com/snakemake/snakemake-wrappers/commit/3722de7000d0b74a3c56bfdb27aad6cf318562ee))
* autobump bio/multiqc
([#2955](https://www.github.com/snakemake/snakemake-wrappers/issues/2955))
([91ad107](https://www.github.com/snakemake/snakemake-wrappers/commit/91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13))
* autobump bio/ngsderive
([#2964](https://www.github.com/snakemake/snakemake-wrappers/issues/2964))
([df82b38](https://www.github.com/snakemake/snakemake-wrappers/commit/df82b381a49b7810087f73b7c83db4fff6d57b66))
* autobump bio/open-cravat/module
([#2966](https://www.github.com/snakemake/snakemake-wrappers/issues/2966))
([f1ffa3e](https://www.github.com/snakemake/snakemake-wrappers/commit/f1ffa3eee366cba828314cc9a368ba69f17d98c2))
* autobump bio/open-cravat/run
([#2965](https://www.github.com/snakemake/snakemake-wrappers/issues/2965))
([9b371ca](https://www.github.com/snakemake/snakemake-wrappers/commit/9b371ca6014a38cf23e78598638e4c709a5e82af))
* autobump bio/ptrimmer
([#2933](https://www.github.com/snakemake/snakemake-wrappers/issues/2933))
([cd37e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/cd37e0bb19e341ad40560828f3c052ef69529088))
* autobump bio/rasusa
([#2967](https://www.github.com/snakemake/snakemake-wrappers/issues/2967))
([9f25643](https://www.github.com/snakemake/snakemake-wrappers/commit/9f2564323429bea84dfb0b01a5b9f53b37fa397c))
* autobump bio/rbt/csvreport
([#2956](https://www.github.com/snakemake/snakemake-wrappers/issues/2956))
([b2a469d](https://www.github.com/snakemake/snakemake-wrappers/commit/b2a469dc907c8f3761399affd29ca53f012cc3ee))
* autobump bio/sambamba/flagstat
([#2973](https://www.github.com/snakemake/snakemake-wrappers/issues/2973))
([4575792](https://www.github.com/snakemake/snakemake-wrappers/commit/4575792deb144dd80401d46bc2fb72175976305a))
* autobump bio/sambamba/index
([#2971](https://www.github.com/snakemake/snakemake-wrappers/issues/2971))
([18359ac](https://www.github.com/snakemake/snakemake-wrappers/commit/18359ac437bb9f1065c703b3bf2da1d3da9548be))
* autobump bio/sambamba/markdup
([#2968](https://www.github.com/snakemake/snakemake-wrappers/issues/2968))
([191542d](https://www.github.com/snakemake/snakemake-wrappers/commit/191542d475853f6f19495e136e105970928a9fd8))
* autobump bio/sambamba/merge
([#2975](https://www.github.com/snakemake/snakemake-wrappers/issues/2975))
([adf9a28](https://www.github.com/snakemake/snakemake-wrappers/commit/adf9a28b64f87aec3fa8286f356f44b6bb77561e))
* autobump bio/sambamba/slice
([#2972](https://www.github.com/snakemake/snakemake-wrappers/issues/2972))
([88ac3f6](https://www.github.com/snakemake/snakemake-wrappers/commit/88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02))
* autobump bio/sambamba/sort
([#2976](https://www.github.com/snakemake/snakemake-wrappers/issues/2976))
([990e841](https://www.github.com/snakemake/snakemake-wrappers/commit/990e8416b730267a65ba5a97b71537655bbfe6db))
* autobump bio/sambamba/view
([#2970](https://www.github.com/snakemake/snakemake-wrappers/issues/2970))
([613e55d](https://www.github.com/snakemake/snakemake-wrappers/commit/613e55d915215348651e878fe37f6533e6d77363))
* autobump bio/seqkit
([#2969](https://www.github.com/snakemake/snakemake-wrappers/issues/2969))
([e25b840](https://www.github.com/snakemake/snakemake-wrappers/commit/e25b8409af3cc9e591b5106f1ebb00289f628207))
* autobump bio/sra-tools/fasterq-dump
([#2974](https://www.github.com/snakemake/snakemake-wrappers/issues/2974))
([d8b4b5f](https://www.github.com/snakemake/snakemake-wrappers/commit/d8b4b5fab114c66bf712ee271b00f831a5ed558d))
* autobump bio/unicycler
([#2957](https://www.github.com/snakemake/snakemake-wrappers/issues/2957))
([185ce7e](https://www.github.com/snakemake/snakemake-wrappers/commit/185ce7e4bd6adbdf840effa665f62e358865c8b8))
* autobump bio/vep/annotate
([#2958](https://www.github.com/snakemake/snakemake-wrappers/issues/2958))
([728658d](https://www.github.com/snakemake/snakemake-wrappers/commit/728658d5fae40ea784f7b8d3c567c4f7240ef7c7))
* autobump bio/vep/cache
([#2959](https://www.github.com/snakemake/snakemake-wrappers/issues/2959))
([f4e5b66](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e5b66f8765d09d51d4a640d2d775d781c3018f))
* autobump bio/whatshap/haplotag
([#2934](https://www.github.com/snakemake/snakemake-wrappers/issues/2934))
([f0b638a](https://www.github.com/snakemake/snakemake-wrappers/commit/f0b638a55280c0727ccef5aab24e03b3d565f290))
* Update Datavzrd to 2.36.12
([#2924](https://www.github.com/snakemake/snakemake-wrappers/issues/2924))
([beb9d22](https://www.github.com/snakemake/snakemake-wrappers/commit/beb9d2231c5d59ba74f23f56bbfc5e004aa72331))
* Use samtools collate in fastq separate wrapper
([#2960](https://www.github.com/snakemake/snakemake-wrappers/issues/2960))
([9c8cf81](https://www.github.com/snakemake/snakemake-wrappers/commit/9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d))
---


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>
votti pushed a commit to FroeseLab/snakemake-wrappers that referenced this pull request Jun 22, 2024
…make#2936)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
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-->

<!-- Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* 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 (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Christian Meesters <[email protected]>
votti pushed a commit to FroeseLab/snakemake-wrappers that referenced this pull request Jun 22, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.11.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.2...v3.11.0)
(2024-05-31)


### Features

* add samtools markdup wrapper
([snakemake#2926](https://www.github.com/snakemake/snakemake-wrappers/issues/2926))
([3c86bae](https://www.github.com/snakemake/snakemake-wrappers/commit/3c86baef4586b596c6c3375336828257e8bb815f))
* Add support for regions file and arbitrary FAI/GZI paths
([snakemake#2936](https://www.github.com/snakemake/snakemake-wrappers/issues/2936))
([445b35f](https://www.github.com/snakemake/snakemake-wrappers/commit/445b35f314f035d8248ca84cb16b273b0e65847c))
* add wrapper to samtools collate
([snakemake#2929](https://www.github.com/snakemake/snakemake-wrappers/issues/2929))
([0c7ae27](https://www.github.com/snakemake/snakemake-wrappers/commit/0c7ae27622e45167b9cc1aaf1be238b0d25429b9))
* All ngsderive subcommands
([snakemake#2732](https://www.github.com/snakemake/snakemake-wrappers/issues/2732))
([847ab1d](https://www.github.com/snakemake/snakemake-wrappers/commit/847ab1d918c09908bcdb40fa3413b6dbc88d4803))
* auto infer run mode
([snakemake#2937](https://www.github.com/snakemake/snakemake-wrappers/issues/2937))
([08bd3cd](https://www.github.com/snakemake/snakemake-wrappers/commit/08bd3cd79243c4c0636f88d229667e58595611bd))
* Goleft indexcov
([snakemake#2734](https://www.github.com/snakemake/snakemake-wrappers/issues/2734))
([ebef6f8](https://www.github.com/snakemake/snakemake-wrappers/commit/ebef6f8259e89d9a06b2264a5d0a34da23d2e84e))


### Bug Fixes

* bamcoverage without effective genome size
([snakemake#2941](https://www.github.com/snakemake/snakemake-wrappers/issues/2941))
([b6ad55f](https://www.github.com/snakemake/snakemake-wrappers/commit/b6ad55f4d2c702ecc904d6b40b4b35b2463c895a))
* issue
[snakemake#366](https://www.github.com/snakemake/snakemake-wrappers/issues/366)
and
[snakemake#2649](https://www.github.com/snakemake/snakemake-wrappers/issues/2649)
([snakemake#2928](https://www.github.com/snakemake/snakemake-wrappers/issues/2928))
([e10ab57](https://www.github.com/snakemake/snakemake-wrappers/commit/e10ab571a63b36ce1295e50b6f6b7e4742e0beae))
* remove NA string replacement, fixed upstream
([snakemake#2940](https://www.github.com/snakemake/snakemake-wrappers/issues/2940))
([8f4d223](https://www.github.com/snakemake/snakemake-wrappers/commit/8f4d223ec6c1e1e2715708d0532399ede4ed2727))


### Performance Improvements

* autobump bio/bismark/bam2nuc
([snakemake#2943](https://www.github.com/snakemake/snakemake-wrappers/issues/2943))
([9228479](https://www.github.com/snakemake/snakemake-wrappers/commit/9228479896c2410ae6a58849bf59e5f01bc5e712))
* autobump bio/bismark/bismark
([snakemake#2948](https://www.github.com/snakemake/snakemake-wrappers/issues/2948))
([d9abb20](https://www.github.com/snakemake/snakemake-wrappers/commit/d9abb20e0e002d9ec16507d86211b0555a2546ba))
* autobump bio/bismark/bismark_genome_preparation
([snakemake#2945](https://www.github.com/snakemake/snakemake-wrappers/issues/2945))
([899ae0d](https://www.github.com/snakemake/snakemake-wrappers/commit/899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6))
* autobump bio/bismark/bismark_methylation_extractor
([snakemake#2944](https://www.github.com/snakemake/snakemake-wrappers/issues/2944))
([1b232d2](https://www.github.com/snakemake/snakemake-wrappers/commit/1b232d24816a40f75568bec224eff4e164b3f953))
* autobump bio/bismark/bismark2bedGraph
([snakemake#2947](https://www.github.com/snakemake/snakemake-wrappers/issues/2947))
([ab29098](https://www.github.com/snakemake/snakemake-wrappers/commit/ab29098757c3eef17884f198234ec456e19414f9))
* autobump bio/bismark/bismark2report
([snakemake#2951](https://www.github.com/snakemake/snakemake-wrappers/issues/2951))
([13dd155](https://www.github.com/snakemake/snakemake-wrappers/commit/13dd155a20025b8aaaa80ce3747e6822562bb6b1))
* autobump bio/bismark/bismark2summary
([snakemake#2946](https://www.github.com/snakemake/snakemake-wrappers/issues/2946))
([bfb3d30](https://www.github.com/snakemake/snakemake-wrappers/commit/bfb3d305daa519faee4ad4ea7dbd313941f4c128))
* autobump bio/bismark/deduplicate_bismark
([snakemake#2950](https://www.github.com/snakemake/snakemake-wrappers/issues/2950))
([bcf3c06](https://www.github.com/snakemake/snakemake-wrappers/commit/bcf3c06887443dae9749254f0e8d34e30f880b7e))
* autobump bio/bowtie2/align
([snakemake#2949](https://www.github.com/snakemake/snakemake-wrappers/issues/2949))
([6b0593f](https://www.github.com/snakemake/snakemake-wrappers/commit/6b0593facfcae0b9c92cb1f31423426752c0230d))
* autobump bio/bowtie2/build
([snakemake#2942](https://www.github.com/snakemake/snakemake-wrappers/issues/2942))
([5b3ca20](https://www.github.com/snakemake/snakemake-wrappers/commit/5b3ca20635bd0e427a548e68cd8a40fdb0047f10))
* autobump bio/bwa-mem2/mem-samblaster
([snakemake#2962](https://www.github.com/snakemake/snakemake-wrappers/issues/2962))
([ff613f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ff613f37f857f23d19e4dc0cace22b02113a7e07))
* autobump bio/bwa/mem-samblaster
([snakemake#2961](https://www.github.com/snakemake/snakemake-wrappers/issues/2961))
([83754dd](https://www.github.com/snakemake/snakemake-wrappers/commit/83754dd9f158ea978faa1ed33668a6dda648cdb7))
* autobump bio/fastq_screen
([snakemake#2952](https://www.github.com/snakemake/snakemake-wrappers/issues/2952))
([e45fcac](https://www.github.com/snakemake/snakemake-wrappers/commit/e45fcac221ef45f345a516bff905a53c864e7355))
* autobump bio/freebayes
([snakemake#2963](https://www.github.com/snakemake/snakemake-wrappers/issues/2963))
([7a0d553](https://www.github.com/snakemake/snakemake-wrappers/commit/7a0d553e09921cebc77b54d314c211b91099f7bd))
* autobump bio/gatk/applybqsr
([snakemake#2938](https://www.github.com/snakemake/snakemake-wrappers/issues/2938))
([498c67f](https://www.github.com/snakemake/snakemake-wrappers/commit/498c67fb12691b0021a7b234dfc279957b46708c))
* autobump bio/gatk3/realignertargetcreator
([snakemake#2931](https://www.github.com/snakemake/snakemake-wrappers/issues/2931))
([2d2835c](https://www.github.com/snakemake/snakemake-wrappers/commit/2d2835c51f974f7f45420f832b8084520d2d3ec0))
* autobump bio/gdc-api/bam-slicing
([snakemake#2954](https://www.github.com/snakemake/snakemake-wrappers/issues/2954))
([32d25c1](https://www.github.com/snakemake/snakemake-wrappers/commit/32d25c1560b4c581694c49dc6d3a596e5ca581ab))
* autobump bio/goleft/indexcov
([snakemake#2930](https://www.github.com/snakemake/snakemake-wrappers/issues/2930))
([5ccbdb0](https://www.github.com/snakemake/snakemake-wrappers/commit/5ccbdb078a835ad0c2fd3e9e63677103fe216eeb))
* autobump bio/gseapy/gsea
([snakemake#2953](https://www.github.com/snakemake/snakemake-wrappers/issues/2953))
([dda3d16](https://www.github.com/snakemake/snakemake-wrappers/commit/dda3d16c9b49145bd58d287db1021c41d5a24710))
* autobump bio/hifiasm
([snakemake#2932](https://www.github.com/snakemake/snakemake-wrappers/issues/2932))
([3722de7](https://www.github.com/snakemake/snakemake-wrappers/commit/3722de7000d0b74a3c56bfdb27aad6cf318562ee))
* autobump bio/multiqc
([snakemake#2955](https://www.github.com/snakemake/snakemake-wrappers/issues/2955))
([91ad107](https://www.github.com/snakemake/snakemake-wrappers/commit/91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13))
* autobump bio/ngsderive
([snakemake#2964](https://www.github.com/snakemake/snakemake-wrappers/issues/2964))
([df82b38](https://www.github.com/snakemake/snakemake-wrappers/commit/df82b381a49b7810087f73b7c83db4fff6d57b66))
* autobump bio/open-cravat/module
([snakemake#2966](https://www.github.com/snakemake/snakemake-wrappers/issues/2966))
([f1ffa3e](https://www.github.com/snakemake/snakemake-wrappers/commit/f1ffa3eee366cba828314cc9a368ba69f17d98c2))
* autobump bio/open-cravat/run
([snakemake#2965](https://www.github.com/snakemake/snakemake-wrappers/issues/2965))
([9b371ca](https://www.github.com/snakemake/snakemake-wrappers/commit/9b371ca6014a38cf23e78598638e4c709a5e82af))
* autobump bio/ptrimmer
([snakemake#2933](https://www.github.com/snakemake/snakemake-wrappers/issues/2933))
([cd37e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/cd37e0bb19e341ad40560828f3c052ef69529088))
* autobump bio/rasusa
([snakemake#2967](https://www.github.com/snakemake/snakemake-wrappers/issues/2967))
([9f25643](https://www.github.com/snakemake/snakemake-wrappers/commit/9f2564323429bea84dfb0b01a5b9f53b37fa397c))
* autobump bio/rbt/csvreport
([snakemake#2956](https://www.github.com/snakemake/snakemake-wrappers/issues/2956))
([b2a469d](https://www.github.com/snakemake/snakemake-wrappers/commit/b2a469dc907c8f3761399affd29ca53f012cc3ee))
* autobump bio/sambamba/flagstat
([snakemake#2973](https://www.github.com/snakemake/snakemake-wrappers/issues/2973))
([4575792](https://www.github.com/snakemake/snakemake-wrappers/commit/4575792deb144dd80401d46bc2fb72175976305a))
* autobump bio/sambamba/index
([snakemake#2971](https://www.github.com/snakemake/snakemake-wrappers/issues/2971))
([18359ac](https://www.github.com/snakemake/snakemake-wrappers/commit/18359ac437bb9f1065c703b3bf2da1d3da9548be))
* autobump bio/sambamba/markdup
([snakemake#2968](https://www.github.com/snakemake/snakemake-wrappers/issues/2968))
([191542d](https://www.github.com/snakemake/snakemake-wrappers/commit/191542d475853f6f19495e136e105970928a9fd8))
* autobump bio/sambamba/merge
([snakemake#2975](https://www.github.com/snakemake/snakemake-wrappers/issues/2975))
([adf9a28](https://www.github.com/snakemake/snakemake-wrappers/commit/adf9a28b64f87aec3fa8286f356f44b6bb77561e))
* autobump bio/sambamba/slice
([snakemake#2972](https://www.github.com/snakemake/snakemake-wrappers/issues/2972))
([88ac3f6](https://www.github.com/snakemake/snakemake-wrappers/commit/88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02))
* autobump bio/sambamba/sort
([snakemake#2976](https://www.github.com/snakemake/snakemake-wrappers/issues/2976))
([990e841](https://www.github.com/snakemake/snakemake-wrappers/commit/990e8416b730267a65ba5a97b71537655bbfe6db))
* autobump bio/sambamba/view
([snakemake#2970](https://www.github.com/snakemake/snakemake-wrappers/issues/2970))
([613e55d](https://www.github.com/snakemake/snakemake-wrappers/commit/613e55d915215348651e878fe37f6533e6d77363))
* autobump bio/seqkit
([snakemake#2969](https://www.github.com/snakemake/snakemake-wrappers/issues/2969))
([e25b840](https://www.github.com/snakemake/snakemake-wrappers/commit/e25b8409af3cc9e591b5106f1ebb00289f628207))
* autobump bio/sra-tools/fasterq-dump
([snakemake#2974](https://www.github.com/snakemake/snakemake-wrappers/issues/2974))
([d8b4b5f](https://www.github.com/snakemake/snakemake-wrappers/commit/d8b4b5fab114c66bf712ee271b00f831a5ed558d))
* autobump bio/unicycler
([snakemake#2957](https://www.github.com/snakemake/snakemake-wrappers/issues/2957))
([185ce7e](https://www.github.com/snakemake/snakemake-wrappers/commit/185ce7e4bd6adbdf840effa665f62e358865c8b8))
* autobump bio/vep/annotate
([snakemake#2958](https://www.github.com/snakemake/snakemake-wrappers/issues/2958))
([728658d](https://www.github.com/snakemake/snakemake-wrappers/commit/728658d5fae40ea784f7b8d3c567c4f7240ef7c7))
* autobump bio/vep/cache
([snakemake#2959](https://www.github.com/snakemake/snakemake-wrappers/issues/2959))
([f4e5b66](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e5b66f8765d09d51d4a640d2d775d781c3018f))
* autobump bio/whatshap/haplotag
([snakemake#2934](https://www.github.com/snakemake/snakemake-wrappers/issues/2934))
([f0b638a](https://www.github.com/snakemake/snakemake-wrappers/commit/f0b638a55280c0727ccef5aab24e03b3d565f290))
* Update Datavzrd to 2.36.12
([snakemake#2924](https://www.github.com/snakemake/snakemake-wrappers/issues/2924))
([beb9d22](https://www.github.com/snakemake/snakemake-wrappers/commit/beb9d2231c5d59ba74f23f56bbfc5e004aa72331))
* Use samtools collate in fastq separate wrapper
([snakemake#2960](https://www.github.com/snakemake/snakemake-wrappers/issues/2960))
([9c8cf81](https://www.github.com/snakemake/snakemake-wrappers/commit/9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d))
---


This PR was generated with [Release
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Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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