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add module for pneumocat#3592

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SPPearce merged 6 commits into
nf-core:masterfrom
rpetit3:rp3-add-pneumocat
Oct 4, 2023
Merged

add module for pneumocat#3592
SPPearce merged 6 commits into
nf-core:masterfrom
rpetit3:rp3-add-pneumocat

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@rpetit3

@rpetit3 rpetit3 commented Jul 4, 2023 •
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PR checklist

Closes #3591

  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

I went with a stub run as this tool will fail if a serotype is not predicted.

SPPearce
SPPearce approved these changes Oct 4, 2023
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Comment thread tests/modules/nf-core/pneumocat/test.yml

@SPPearce SPPearce Oct 4, 2023

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I see this is a stub test, have you checked it works correctly locally?

@SPPearce SPPearce added this pull request to the merge queue Oct 4, 2023
Merged via the queue into nf-core:master with commit 43988a1 Oct 4, 2023
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Oct 16, 2023
@rpetit3 @SPPearce
add module for pneumocat (nf-core#3592)
9ffd0cb 
* add module for pneumocat

* make prettier

* change scope of VERSION

* Update test.yml

* Update main.nf

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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new module: PneumoCAT

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@rpetit3 @SPPearce