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Issue 168 deal properly with download of data #191

Merged
merged 6 commits into from
Oct 11, 2023
Merged

Issue 168 deal properly with download of data #191

merged 6 commits into from
Oct 11, 2023

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tfalkarkea
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PR checklist

  • This comment contains a description of changes (with reason).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Adjusted three subworkflows (Eggnog, EUKulele, Kofam) to not download databases when a valid database is provided by the user with command line arguments. Documentation updated to indicate this ability. Working off of this issue: #168

@danilodileo
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danilodileo commented Oct 3, 2023 •
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Hello and well done! @tfalkarkea
For me, eggnog and kofamscan are perfect as they are now. The only comment is about eukulele. Last week we decided to skip eukulele_download module as it doesn't caching correctly. 2 concerns: when´-resume´ the pipeline, the analysis will start again and we want avoid this kind of behavior - the module doesn't work on some compute infrastructure (tower).

If you look in PR #190 you can see what we proposed. Eukulele_search is able to check the presence of the directory and the files by its own so we can skip the checks that you improved in the subworkflow.

What I will suggest are two options:

  • Check whether your code is working with the behaviour that we expect (it runs on Tower and "resume" is working). if it is so, I will approve this PR.
  • Just remove the changes from eukulele subworkflow (+ in the main workflow for eukulele) then we can merge the two PRs.

Thanks a lot for your contribution!

danilodileo
danilodileo reviewed Oct 5, 2023
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See previous comment.

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github-actions bot commented Oct 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cdde51d

+| ✅ 156 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 03:30:10

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danilodileo commented Oct 11, 2023 •
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Hi @tfalkarkea since you have not time to contribute, I took the lead and clear the PR so we can merge it. I decided to go for the second option and I removed the two-steps module for eukulele. Thanks for you help, we really appreciate it 🤩. We will try to find a way to test the pipeline on Tower in a second moment (probably in two weeks at the hackathon!).

Cheers!

danilodileo
danilodileo approved these changes Oct 11, 2023
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LGTM

@danilodileo danilodileo merged commit 26d91c7 into nf-core:dev Oct 11, 2023
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@danilodileo danilodileo danilodileo approved these changes

@erikrikarddaniel erikrikarddaniel Awaiting requested review from erikrikarddaniel

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@tfalkarkea @danilodileo