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feat: Add wrapper for ROOT hadd #2785

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merged 12 commits into from Apr 4, 2024

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GoodingJamie
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@GoodingJamie GoodingJamie commented Apr 3, 2024

Adds a wrapper for the hadd utility in the ROOT software package used primarily in High Energy Physics. Since this is the first physics wrapper, the top-level category phys is also added here.

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).

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@GoodingJamie
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Thanks a lot for the review @fgvieira 😄

@fgvieira
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fgvieira commented Apr 4, 2024

Sure! Can you just add the tests to test.py?
Otherwise it looks quite good.

@GoodingJamie
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I've added the test to test.py (which passes in CI) and included the pinned environment. From my side this is good to go 😄

@fgvieira
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fgvieira commented Apr 4, 2024

Cool, and thanks for your contribution!

@fgvieira fgvieira merged commit 3e82e9c into snakemake:master Apr 4, 2024
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johanneskoester pushed a commit that referenced this pull request Apr 12, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.8.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.7.0...v3.8.0)
(2024-04-12)


### Features

* add fgbio sorting to bwa mem
([#2805](https://www.github.com/snakemake/snakemake-wrappers/issues/2805))
([af98a55](https://www.github.com/snakemake/snakemake-wrappers/commit/af98a5591bc841b7fc829bcf71b9e4b2ebfe29d0))
* Add wrapper for ROOT hadd
([#2785](https://www.github.com/snakemake/snakemake-wrappers/issues/2785))
([3e82e9c](https://www.github.com/snakemake/snakemake-wrappers/commit/3e82e9cd8a601d41381a870aee16cbdfb5072459))


### Bug Fixes

* bcftool stats bug
([#2806](https://www.github.com/snakemake/snakemake-wrappers/issues/2806))
([e7ff82c](https://www.github.com/snakemake/snakemake-wrappers/commit/e7ff82cbe32d7ec8e296be3e21cb0653c3f1095d))


### Performance Improvements

* autobump bio/busco
([#2787](https://www.github.com/snakemake/snakemake-wrappers/issues/2787))
([ebe243e](https://www.github.com/snakemake/snakemake-wrappers/commit/ebe243e751f40712bf3953a49c95d510b3680f14))
* autobump bio/deeptools/plotfingerprint
([#2776](https://www.github.com/snakemake/snakemake-wrappers/issues/2776))
([214ea28](https://www.github.com/snakemake/snakemake-wrappers/commit/214ea28825991192f4f5f25b25f554eadfb15ec9))
* autobump bio/deeptools/plotheatmap
([#2788](https://www.github.com/snakemake/snakemake-wrappers/issues/2788))
([81ee08b](https://www.github.com/snakemake/snakemake-wrappers/commit/81ee08b767737e66f4ef843fa7606d68d082e737))
* autobump bio/ega/fetch
([#2789](https://www.github.com/snakemake/snakemake-wrappers/issues/2789))
([fd83ecb](https://www.github.com/snakemake/snakemake-wrappers/commit/fd83ecbeed2a36adc1170a41de59ed50202ee2e9))
* autobump bio/freebayes
([#1850](https://www.github.com/snakemake/snakemake-wrappers/issues/1850))
([795e778](https://www.github.com/snakemake/snakemake-wrappers/commit/795e7781331c4e4bba56f055bc9c27d2b2167955))
* autobump bio/freebayes
([#2790](https://www.github.com/snakemake/snakemake-wrappers/issues/2790))
([fe5de66](https://www.github.com/snakemake/snakemake-wrappers/commit/fe5de660110c8131d17ee27873a9c7f553133b36))
* autobump bio/gdc-api/bam-slicing
([#2778](https://www.github.com/snakemake/snakemake-wrappers/issues/2778))
([9375ca8](https://www.github.com/snakemake/snakemake-wrappers/commit/9375ca8c718faf4b789633c5db768d247b59e93a))
* autobump bio/minimap2/aligner
([#2780](https://www.github.com/snakemake/snakemake-wrappers/issues/2780))
([23fd5a3](https://www.github.com/snakemake/snakemake-wrappers/commit/23fd5a325964c7121ddeb218bad64630675e04db))
* autobump bio/minimap2/index
([#2779](https://www.github.com/snakemake/snakemake-wrappers/issues/2779))
([8f5d611](https://www.github.com/snakemake/snakemake-wrappers/commit/8f5d61190bb7a711bba55e0c4591a8829e659964))
* autobump bio/plass
([#2791](https://www.github.com/snakemake/snakemake-wrappers/issues/2791))
([11f34ca](https://www.github.com/snakemake/snakemake-wrappers/commit/11f34cad50399510051025aa157a4541ccb0b0f0))
* autobump bio/rseqc/read_gc
([#2781](https://www.github.com/snakemake/snakemake-wrappers/issues/2781))
([842998d](https://www.github.com/snakemake/snakemake-wrappers/commit/842998dee3c213a4db315c472a98f5781734b394))
* autobump bio/seqkit
([#2795](https://www.github.com/snakemake/snakemake-wrappers/issues/2795))
([1b2e7ba](https://www.github.com/snakemake/snakemake-wrappers/commit/1b2e7ba1b1163189cb617257a49f3e7492738f43))
* autobump bio/sourmash/compute
([#2794](https://www.github.com/snakemake/snakemake-wrappers/issues/2794))
([8a37a3e](https://www.github.com/snakemake/snakemake-wrappers/commit/8a37a3e4fc29e3d63d8aa7d83cd9467382c4906d))
* autobump bio/tabix/query
([#2796](https://www.github.com/snakemake/snakemake-wrappers/issues/2796))
([e21217e](https://www.github.com/snakemake/snakemake-wrappers/commit/e21217ebc139147e72424cd0a607907a3bf7f613))
* autobump bio/tmb/pytmb
([#2797](https://www.github.com/snakemake/snakemake-wrappers/issues/2797))
([28ae8a8](https://www.github.com/snakemake/snakemake-wrappers/commit/28ae8a8d199235951617d164394e762b0453ebf9))
* autobump bio/ucsc/gtfToGenePred
([#2782](https://www.github.com/snakemake/snakemake-wrappers/issues/2782))
([4e8c925](https://www.github.com/snakemake/snakemake-wrappers/commit/4e8c9252995e7ab3773c6dff6aee5e881bb2192f))
* autobump bio/unicycler
([#2316](https://www.github.com/snakemake/snakemake-wrappers/issues/2316))
([0d1486b](https://www.github.com/snakemake/snakemake-wrappers/commit/0d1486b0b88b0f0077faf7533dc5d8b422e3af4d))
* autobump bio/vembrane/filter
([#2783](https://www.github.com/snakemake/snakemake-wrappers/issues/2783))
([bb271ab](https://www.github.com/snakemake/snakemake-wrappers/commit/bb271abf6dbce49a9e86b5d299b2be8b0fca6df6))
* autobump bio/vembrane/table
([#2784](https://www.github.com/snakemake/snakemake-wrappers/issues/2784))
([491d5b6](https://www.github.com/snakemake/snakemake-wrappers/commit/491d5b6273d8b341c1c9a898253ab196598a8b0a))
* autobump bio/vg/construct
([#2798](https://www.github.com/snakemake/snakemake-wrappers/issues/2798))
([25300e4](https://www.github.com/snakemake/snakemake-wrappers/commit/25300e40f0b37ddc2e2c46534ef678b0a84d41c6))
* autobump bio/vg/ids
([#2804](https://www.github.com/snakemake/snakemake-wrappers/issues/2804))
([4162ce1](https://www.github.com/snakemake/snakemake-wrappers/commit/4162ce1926b7bb2d5bdfa31315597f18125db791))
* autobump bio/vg/kmers
([#2802](https://www.github.com/snakemake/snakemake-wrappers/issues/2802))
([9ddb88d](https://www.github.com/snakemake/snakemake-wrappers/commit/9ddb88d768a061b3dd9b3815c838fd5495b721b4))
* autobump bio/vg/merge
([#2800](https://www.github.com/snakemake/snakemake-wrappers/issues/2800))
([5ba8325](https://www.github.com/snakemake/snakemake-wrappers/commit/5ba8325e54730a42096f29dc286de8fc615ed5ff))
* autobump bio/vg/prune
([#2801](https://www.github.com/snakemake/snakemake-wrappers/issues/2801))
([2061beb](https://www.github.com/snakemake/snakemake-wrappers/commit/2061beb06a5bbf29ff5e095e1ac5803801a0fa22))
* autobump bio/vg/sim
([#2799](https://www.github.com/snakemake/snakemake-wrappers/issues/2799))
([dfb0d6b](https://www.github.com/snakemake/snakemake-wrappers/commit/dfb0d6bf4f01bca68e221a08f08ed47fbaa739d4))
* autobump bio/vsearch
([#2803](https://www.github.com/snakemake/snakemake-wrappers/issues/2803))
([7070607](https://www.github.com/snakemake/snakemake-wrappers/commit/7070607cb4e8bc233a55e20b62a2f019e63c9b00))
---


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>
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