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New module: regtools junction extract #7033

Merged
merged 21 commits into from
Nov 20, 2024
Merged

New module: regtools junction extract #7033

merged 21 commits into from
Nov 20, 2024

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abartlett004
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PR checklist

New module for regtools junction extract

Closes #7032

  • 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

@mashehu mashehu changed the title initial commit New module: regtools junction extract Nov 20, 2024
@lpantano lpantano self-requested a review November 20, 2024 14:31
@lpantano lpantano marked this pull request as ready for review November 20, 2024 14:58
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@mashehu, can you take a quick look in case we are missing something? thanks!

mahesh-panchal
mahesh-panchal reviewed Nov 20, 2024
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Linting fails: nf-core modules lint regtools/junctionsextract

SPPearce
SPPearce approved these changes Nov 20, 2024
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One little thing, the stub versions is wrong at the moment.

modules/nf-core/regtools/junctionsextract/main.nf Outdated Show resolved Hide resolved
SPPearce
SPPearce requested changes Nov 20, 2024
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Actually, you aren't checking the versions at all? How did that not fail the linting?

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Linting fails: nf-core modules lint regtools/junctionsextract

And it didn't run at all?

edmundmiller
edmundmiller requested changes Nov 20, 2024
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Just started looking into this because it should've triggered the wave CI, but it didn't 🙃

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SPPearce commented Nov 20, 2024 •
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@edmundmiller, while you are here can you check why nf-core modules lint didn't notice the lack of versions (or wasn't ran at all)?

@edmundmiller edmundmiller self-requested a review November 20, 2024 17:51
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Just started looking into this because it should've triggered the wave CI, but it didn't 🙃

Ah, it's coming from a fork, and that's why.

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@SPPearce, do you have any other comment?

@lpantano lpantano requested a review from SPPearce November 20, 2024 19:26
@edmundmiller edmundmiller mentioned this pull request Nov 20, 2024
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Updated the regex and tested the versions.

Gonna skip the CI on this one, should be fixed in #7043

@edmundmiller edmundmiller merged commit 0461b3e into nf-core:master Nov 20, 2024
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@abartlett004 abartlett004 deleted the regtools branch November 20, 2024 19:52
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@SPPearce, do you have any other comment?

No, happy now (although as Edmund had approved that was sufficient)

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@mahesh-panchal mahesh-panchal mahesh-panchal left review comments

@edmundmiller edmundmiller edmundmiller approved these changes

@lpantano lpantano lpantano approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

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new module:regtools
5 participants
@abartlett004 @lpantano @SPPearce @edmundmiller @mahesh-panchal