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Don't force same KMCP mode for all database #493

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Merged
merged 2 commits into from
Jun 11, 2024
Merged

Don't force same KMCP mode for all database #493

merged 2 commits into from
Jun 11, 2024

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jfy133
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@jfy133 jfy133 commented Jun 10, 2024

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 124a9c9

+| ✅ 257 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-10 12:48:30

@sofstam sofstam self-requested a review June 10, 2024 14:32
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sofstam approved these changes Jun 11, 2024
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🚀

Shall the kmcp mode be documented in docs? I realised it was not there.

subworkflows/local/profiling.nf
}

KMCP_SEARCH ( ch_input_for_kmcp.db, ch_input_for_kmcp.reads )
KMCP_SEARCH ( ch_input_for_kmcp.reads, ch_input_for_kmcp.db )
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Good catch!

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I flipped it in the module update 😬

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Yes, I saw it.

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jfy133 commented Jun 11, 2024

🚀

Shall the kmcp mode be documented in docs? I realised it was not there.

@sofstam what do you mean exactly? I would assume people would have to look up the settings of the particualar tool they are interested in anyway to know what to put in the db_params of the database sheet?

@jfy133 jfy133 merged commit 5da74cf into dev Jun 11, 2024
@jfy133 jfy133 deleted the kmcp-dont-force-mode branch June 11, 2024 14:15
@jfy133 jfy133 mentioned this pull request Jun 11, 2024
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@sofstam sofstam mentioned this pull request Jun 13, 2024
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@jfy133 @sofstam
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