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Added .ngc support for sratools fasterqdump and prefetch #4303

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merged 12 commits into from
Nov 17, 2023

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alexblaessle
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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

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@Midnighter Midnighter left a comment

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Looks good. I think you can drop one level of conditionals, since a missing file will just end in the final else clause anyway, but it's certainly fine like this.

modules/nf-core/sratools/fasterqdump/main.nf Outdated Show resolved Hide resolved
@apeltzer
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ping @maxulysse to the rescue :D - this will be useful for nf-core/fetchngs#238 too

@maxulysse
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ok, so as far as I can tell, the pair end tests are not working, but I'm fairly sure it's unrelated to your PR @alexblaessle, I'll have a look and try to come up with a separate PR to fix that so that we can merge your PR.
Expect a fix by the end of the day.

@maxulysse
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#4355 will solve the tests, sorry about that

@apeltzer apeltzer added this pull request to the merge queue Nov 17, 2023
Merged via the queue into nf-core:master with commit b1d2002 Nov 17, 2023
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@alexblaessle
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Thanks for all the help @apeltzer @maxulysse @Midnighter

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4 participants