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add module for midas/run #2696

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Merged
merged 5 commits into from
Mar 7, 2023
Merged

add module for midas/run #2696

merged 5 commits into from
Mar 7, 2023

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rpetit3
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@rpetit3 rpetit3 commented Dec 23, 2022 •
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PR checklist

Closes #2695

  • 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

MIDAS requires a >30GB database, so had to go with a stub-run. Will have a rull test on the Bactopia side

@rpetit3
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rpetit3 commented Dec 28, 2022

Doing testing locally. Have a PR in at Bioconda to fix the container: bioconda/bioconda-recipes#38566

@rpetit3 rpetit3 marked this pull request as draft December 28, 2022 16:02
@rpetit3 rpetit3 marked this pull request as ready for review December 29, 2022 18:31
nvnieuwk
nvnieuwk approved these changes Jan 2, 2023
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A small comment otherwise LGTM

modules/nf-core/midas/run/main.nf
@@ -0,0 +1,71 @@
VERSION = '1.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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The VERSION variable should be inside the script part of the module, see: https://nf-co.re/docs/contributing/modules#general paragraph 4 :)

@matthdsm matthdsm merged commit 6e5f7d6 into nf-core:master Mar 7, 2023
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

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new module: midas/run
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@rpetit3 @nvnieuwk @matthdsm