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Add module muse/sump #5629

Merged
merged 21 commits into from
Dec 2, 2024
Merged

Add module muse/sump #5629

merged 21 commits into from
Dec 2, 2024

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famosab
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@famosab famosab commented May 17, 2024 •
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PR checklist

Closes #5621

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@famosab famosab requested a review from a team as a code owner May 17, 2024 14:16
@famosab famosab requested review from vagkaratzas and removed request for a team May 17, 2024 14:16
@famosab famosab changed the title Add module muse/sump and Dockerfile Add module muse/sump May 17, 2024
@famosab famosab mentioned this pull request May 17, 2024
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@maxulysse
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I would rather we fix https://bioconda.github.io/recipes/muse/README.html
And update it to use the latest versions in https://github.com/wwylab/MuSE

@famosab
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famosab commented May 21, 2024

I opened a PR: bioconda/bioconda-recipes#47957

@famosab famosab requested a review from a team as a code owner November 15, 2024 09:30
SPPearce
SPPearce reviewed Nov 15, 2024
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@famosab famosab requested a review from SPPearce November 15, 2024 12:23
SPPearce
SPPearce reviewed Nov 16, 2024
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@famosab famosab requested a review from SPPearce November 29, 2024 13:18
SPPearce
SPPearce approved these changes Dec 2, 2024
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Ok, looks good to me now then

@famosab famosab added this pull request to the merge queue Dec 2, 2024
Merged via the queue into nf-core:master with commit 8e17f28 Dec 2, 2024
30 checks passed
@famosab famosab deleted the muse-sump branch December 2, 2024 23:08
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@famosab @SPPearce
Add module muse/sump (nf-core#5629)
2ebe102 
* start work on muse/sump

* update to include tbi

* uodate snap

* update paths

* prettier

* exclude conda test

* change to bioconda

* update meta and snap

* add conda test

* update tests

* change ext args to new convention

* update containers and version extraction and add gzip

* add bgzip

* Update modules/nf-core/muse/sump/meta.yml

Co-authored-by: Simon Pearce <[email protected]>

* update test

* finalize bgzip and specify tests

* fix meta

---------

Co-authored-by: Simon Pearce <[email protected]>
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@mashehu mashehu mashehu left review comments

@SPPearce SPPearce SPPearce approved these changes

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas vagkaratzas was automatically assigned from nf-core/nf-test

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new module: MuSE
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@famosab @maxulysse @mashehu @SPPearce