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Update ANTISMASH to 6.1.1 and enable_conda replacement #2688

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merged 10 commits into from
Dec 21, 2022
Merged

Update ANTISMASH to 6.1.1 and enable_conda replacement #2688

merged 10 commits into from
Dec 21, 2022

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jfy133
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@jfy133 jfy133 commented Dec 21, 2022

This updates

  • ANTISMASH to 6.1.1 (fixing jinja import errors)
  • Uses a new method of detecting whether conda is being used or not to correctly set paths for downloading

Note: it's still not ideal as may not work for locally instlaled tool pipeline runs (i.e., without conda/docker/singularity) but we don't really want this in nf-core as it's against reproducibilty

PR checklist

Closes #XXX

  • 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

@jfy133 jfy133 requested a review from jasmezz December 21, 2022 11:03
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@nvnieuwk nvnieuwk left a comment

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Looks like an awesome solution 🥳 (if all tests pass of course)

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@jasmezz jasmezz left a comment

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Thanks James, this looks good!

@jfy133 jfy133 merged commit 591bb22 into nf-core:master Dec 21, 2022
@jfy133 jfy133 deleted the antismash-conda-fix branch December 21, 2022 17:10
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3 participants