Merge branch 'snakemake:master' into master

.github/pull_request_template.md

@@ -6,22 +6,12 @@
 ### QC
 <!-- Make sure that you can tick the boxes below. -->
 
-* [ ] I confirm that:
+* [ ] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).
 
-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).
+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

CHANGELOG.md

@@ -1,5 +1,130 @@
 # Changelog
 
+## [4.2.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.1...v4.2.0) (2024-08-23)
+
+
+### Features
+
+* Pcaexplorer pcaplot ([#1728](https://www.github.com/snakemake/snakemake-wrappers/issues/1728)) ([8563e88](https://www.github.com/snakemake/snakemake-wrappers/commit/8563e882e61ddad7db6386f65803d13a6c1926af))
+
+
+### Performance Improvements
+
+* autobump bio/bbtools ([#3127](https://www.github.com/snakemake/snakemake-wrappers/issues/3127)) ([a9bd6df](https://www.github.com/snakemake/snakemake-wrappers/commit/a9bd6dfdeee5692c76507148e12e81547c0c0906))
+* autobump bio/gatk3/printreads ([#3129](https://www.github.com/snakemake/snakemake-wrappers/issues/3129)) ([97b2c9d](https://www.github.com/snakemake/snakemake-wrappers/commit/97b2c9d218b120cda5991303f7b1b3d5b854bf2f))
+* autobump bio/last/lastal ([#3131](https://www.github.com/snakemake/snakemake-wrappers/issues/3131)) ([2c13329](https://www.github.com/snakemake/snakemake-wrappers/commit/2c1332948b3082438fd2021087592b47a48c8a5c))
+* autobump bio/last/lastdb ([#3130](https://www.github.com/snakemake/snakemake-wrappers/issues/3130)) ([ce9dfd4](https://www.github.com/snakemake/snakemake-wrappers/commit/ce9dfd459862a86fa0cb960708e232d21894bd60))
+* autobump bio/multiqc ([#3132](https://www.github.com/snakemake/snakemake-wrappers/issues/3132)) ([b5bb552](https://www.github.com/snakemake/snakemake-wrappers/commit/b5bb55238100f1f4c520d173323ce4c84e035cbb))
+* autobump bio/reference/ensembl-mysql-table ([#3133](https://www.github.com/snakemake/snakemake-wrappers/issues/3133)) ([065d45e](https://www.github.com/snakemake/snakemake-wrappers/commit/065d45eba68db3375213095ecf2332705b333cf0))
+
+### [4.1.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.0...v4.1.1) (2024-08-21)
+
+
+### Bug Fixes
+
+* Fix datavzrd wrapper ([#3125](https://www.github.com/snakemake/snakemake-wrappers/issues/3125)) ([5bd032c](https://www.github.com/snakemake/snakemake-wrappers/commit/5bd032cfa2a24eaa66cb7e24f5b3439fae939886))
+
+## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21)
+
+
+### Features
+
+* Allow outputting of rendered yte config in Datavzrd wrapper ([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123)) ([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c))
+
+
+### Bug Fixes
+
+* Correctly handle non str index list for bwa-mem2/mem ([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101)) ([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb))
+
+
+### Performance Improvements
+
+* autobump bio/gatk3/baserecalibrator ([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119)) ([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980))
+* autobump bio/gatk3/realignertargetcreator ([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118)) ([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb))
+* autobump bio/genomescope ([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117)) ([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f))
+* autobump bio/igv-reports ([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120)) ([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39))
+* autobump bio/trinity ([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121)) ([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5))
+* Update Datavzrd wrapper ([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122)) ([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88))
+
+## [4.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.2...v4.0.0) (2024-08-14)
+
+
+### ⚠ BREAKING CHANGES
+
+* switch to nonpareil utils script for plotting (#3100)
+
+### Features
+
+* add ensembl mysql table wrapper ([#3103](https://www.github.com/snakemake/snakemake-wrappers/issues/3103)) ([169a315](https://www.github.com/snakemake/snakemake-wrappers/commit/169a31508f330079799842a21d3b555714365041))
+* switch to nonpareil utils script for plotting ([#3100](https://www.github.com/snakemake/snakemake-wrappers/issues/3100)) ([d8ee6cb](https://www.github.com/snakemake/snakemake-wrappers/commit/d8ee6cb1d15537cd8a42c38b9f2116cc77fa2880))
+
+### [3.14.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.1...v3.14.2) (2024-08-13)
+
+
+### Performance Improvements
+
+* autobump bio/cnv_facets ([#2775](https://www.github.com/snakemake/snakemake-wrappers/issues/2775)) ([0c3b69e](https://www.github.com/snakemake/snakemake-wrappers/commit/0c3b69ecbda35b55ca3c9176ceab0df8aea4edc0))
+
+### [3.14.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.0...v3.14.1) (2024-08-09)
+
+
+### Bug Fixes
+
+* add missing raw string in REGEX_RULES ([#3104](https://www.github.com/snakemake/snakemake-wrappers/issues/3104)) ([74a3269](https://www.github.com/snakemake/snakemake-wrappers/commit/74a3269fe7152464e8134d7560a32540e4197977))
+* download already indexed vep cache tarball ([#3102](https://www.github.com/snakemake/snakemake-wrappers/issues/3102)) ([13c6ef7](https://www.github.com/snakemake/snakemake-wrappers/commit/13c6ef74db8f6c4608c87f6209bab69b3e9ed16a))
+
+
+### Performance Improvements
+
+* autobump bio/encode_fastq_downloader ([#3105](https://www.github.com/snakemake/snakemake-wrappers/issues/3105)) ([695ab1b](https://www.github.com/snakemake/snakemake-wrappers/commit/695ab1b1e39ec2a9693ef5f721bc564e50f716e2))
+* autobump bio/gatk3/indelrealigner ([#3106](https://www.github.com/snakemake/snakemake-wrappers/issues/3106)) ([09d6e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/09d6e0b0d0857c88f6f2c81aec3d7714eb9fb738))
+* autobump bio/gdc-api/bam-slicing ([#3096](https://www.github.com/snakemake/snakemake-wrappers/issues/3096)) ([248b611](https://www.github.com/snakemake/snakemake-wrappers/commit/248b611f33ce879ad40eef4b78ad2d84cda43948))
+* autobump bio/last/lastal ([#3108](https://www.github.com/snakemake/snakemake-wrappers/issues/3108)) ([9f7a264](https://www.github.com/snakemake/snakemake-wrappers/commit/9f7a264c5ceb560008945a4520960e219f470827))
+* autobump bio/last/lastdb ([#3107](https://www.github.com/snakemake/snakemake-wrappers/issues/3107)) ([b1c3334](https://www.github.com/snakemake/snakemake-wrappers/commit/b1c333462d4540a4ed995af2a190bdab0f43e66a))
+* autobump bio/mapdamage2 ([#3109](https://www.github.com/snakemake/snakemake-wrappers/issues/3109)) ([a870b8e](https://www.github.com/snakemake/snakemake-wrappers/commit/a870b8ef9bc89a18b093dc6303048b5e1202f740))
+* autobump bio/sourmash/compute ([#3098](https://www.github.com/snakemake/snakemake-wrappers/issues/3098)) ([5796bc6](https://www.github.com/snakemake/snakemake-wrappers/commit/5796bc6fe0908c4922bb8bfc93183df72afa04b2))
+* autobump bio/spades/metaspades ([#3110](https://www.github.com/snakemake/snakemake-wrappers/issues/3110)) ([e7fb075](https://www.github.com/snakemake/snakemake-wrappers/commit/e7fb075ad006c26c407927f37fe6c0e40b15336e))
+* autobump bio/unicycler ([#3099](https://www.github.com/snakemake/snakemake-wrappers/issues/3099)) ([a09832a](https://www.github.com/snakemake/snakemake-wrappers/commit/a09832ae1ada3771d130087bc6dec5656b635643))
+* autobump bio/vembrane/filter ([#3111](https://www.github.com/snakemake/snakemake-wrappers/issues/3111)) ([5ec4df5](https://www.github.com/snakemake/snakemake-wrappers/commit/5ec4df572af0fed2589579cd4bc7be8749d55886))
+* autobump bio/vembrane/table ([#3112](https://www.github.com/snakemake/snakemake-wrappers/issues/3112)) ([9411cc9](https://www.github.com/snakemake/snakemake-wrappers/commit/9411cc94ed21493c62cc4fcd27307a87fe205e34))
+* autobump bio/vep/plugins ([#3113](https://www.github.com/snakemake/snakemake-wrappers/issues/3113)) ([4e7d29b](https://www.github.com/snakemake/snakemake-wrappers/commit/4e7d29b0aba8e20b2df8754d551de81a4c83fb53))
+
+## [3.14.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.8...v3.14.0) (2024-07-31)
+
+
+### Features
+
+* add new wrapper to create annotation tables via Ensembl biomart ([#3072](https://www.github.com/snakemake/snakemake-wrappers/issues/3072)) ([07dc088](https://www.github.com/snakemake/snakemake-wrappers/commit/07dc08890bea0c13056d70f17a247f46c99e00ab))
+
+
+### Performance Improvements
+
+* autobump bio/blast/blastn ([#3080](https://www.github.com/snakemake/snakemake-wrappers/issues/3080)) ([bc0b80d](https://www.github.com/snakemake/snakemake-wrappers/commit/bc0b80db175c25a04cc2c4a3cd665f6be297741b))
+* autobump bio/blast/makeblastdb ([#3078](https://www.github.com/snakemake/snakemake-wrappers/issues/3078)) ([86ec876](https://www.github.com/snakemake/snakemake-wrappers/commit/86ec8769ddb9a881ca28d0b4600e24b5f9d41229))
+* autobump bio/bwa/mem ([#3079](https://www.github.com/snakemake/snakemake-wrappers/issues/3079)) ([01dc16f](https://www.github.com/snakemake/snakemake-wrappers/commit/01dc16fdebfab3ee6f36983a317fc8ea731f1d44))
+* autobump bio/entrez/efetch ([#3081](https://www.github.com/snakemake/snakemake-wrappers/issues/3081)) ([f178d5f](https://www.github.com/snakemake/snakemake-wrappers/commit/f178d5f1da9a8f420a1e1f8f08053f3983dc11e0))
+* autobump bio/fgbio/annotatebamwithumis ([#3082](https://www.github.com/snakemake/snakemake-wrappers/issues/3082)) ([b902adf](https://www.github.com/snakemake/snakemake-wrappers/commit/b902adfb65d0ea18dc557b25aa98031a394a99c8))
+* autobump bio/fgbio/callmolecularconsensusreads ([#3085](https://www.github.com/snakemake/snakemake-wrappers/issues/3085)) ([5727f2d](https://www.github.com/snakemake/snakemake-wrappers/commit/5727f2d1369ee5afe5fe0f3e5a051f81e51b553a))
+* autobump bio/fgbio/collectduplexseqmetrics ([#3084](https://www.github.com/snakemake/snakemake-wrappers/issues/3084)) ([339720c](https://www.github.com/snakemake/snakemake-wrappers/commit/339720c78b04d1b407b171b099f0cbfdba4bf824))
+* autobump bio/fgbio/filterconsensusreads ([#3086](https://www.github.com/snakemake/snakemake-wrappers/issues/3086)) ([1240b48](https://www.github.com/snakemake/snakemake-wrappers/commit/1240b481c4490f698fe1496cb5e129062caac2ed))
+* autobump bio/fgbio/groupreadsbyumi ([#3083](https://www.github.com/snakemake/snakemake-wrappers/issues/3083)) ([333fcdd](https://www.github.com/snakemake/snakemake-wrappers/commit/333fcdd36475f410945eac1d9ba882df0693a542))
+* autobump bio/fgbio/setmateinformation ([#3088](https://www.github.com/snakemake/snakemake-wrappers/issues/3088)) ([f9d678d](https://www.github.com/snakemake/snakemake-wrappers/commit/f9d678d51e1e81e1226f87432b98b510cd70901b))
+* autobump bio/freebayes ([#3087](https://www.github.com/snakemake/snakemake-wrappers/issues/3087)) ([b23c95d](https://www.github.com/snakemake/snakemake-wrappers/commit/b23c95d9d12182f4e6234486b7ce4274272fa8be))
+* autobump bio/gdc-api/bam-slicing ([#3089](https://www.github.com/snakemake/snakemake-wrappers/issues/3089)) ([5de2293](https://www.github.com/snakemake/snakemake-wrappers/commit/5de22930fe0f9fd6e8350bea5000a2c9b50d10d7))
+* autobump bio/nonpareil/infer ([#3092](https://www.github.com/snakemake/snakemake-wrappers/issues/3092)) ([9e1cc99](https://www.github.com/snakemake/snakemake-wrappers/commit/9e1cc9914508fe883d4bfca064282b36fc1399f5))
+* autobump bio/nonpareil/plot ([#3093](https://www.github.com/snakemake/snakemake-wrappers/issues/3093)) ([4b46579](https://www.github.com/snakemake/snakemake-wrappers/commit/4b465798b021e179830bc2ed980f4a5c194fcba2))
+* autobump bio/taxonkit ([#3094](https://www.github.com/snakemake/snakemake-wrappers/issues/3094)) ([6046793](https://www.github.com/snakemake/snakemake-wrappers/commit/60467935840ff3e25cb40c7e16b106ce0fb8b64d))
+* autobump bio/ucsc/gtfToGenePred ([#3095](https://www.github.com/snakemake/snakemake-wrappers/issues/3095)) ([1a4ddaa](https://www.github.com/snakemake/snakemake-wrappers/commit/1a4ddaade208efed101fb66ba9bb398946f7e807))
+* autobump bio/unicycler ([#2987](https://www.github.com/snakemake/snakemake-wrappers/issues/2987)) ([a192628](https://www.github.com/snakemake/snakemake-wrappers/commit/a192628ce9523c0c0523e619571c3ca050187dca))
+* Update Datavzrd wrapper ([#3074](https://www.github.com/snakemake/snakemake-wrappers/issues/3074)) ([9d47dd7](https://www.github.com/snakemake/snakemake-wrappers/commit/9d47dd76995e4baeb2b9ea7b3278cc713e9e4f17))
+
+### [3.13.8](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.7...v3.13.8) (2024-07-18)
+
+
+### Performance Improvements
+
+* update datavzrd 2.41.0 ([5aec56a](https://www.github.com/snakemake/snakemake-wrappers/commit/5aec56a2c9651df40d48605afc71656a3f77d6c1))
+
 ### [3.13.7](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.13.6...v3.13.7) (2024-07-12)