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Add stub and update test #16

Merged
merged 22 commits into from
May 8, 2024
Merged

Add stub and update test #16

merged 22 commits into from
May 8, 2024

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented May 7, 2024 •
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Add stub run to local modules.
Update test.config with correct samplesheet input.
Get rid of parameters inside local modules.
Get rid of unused validateInputParameters function and other "genome" stuff.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented May 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0d9ea01

+| ✅ 184 tests passed       |+
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-07 16:54:45

itrujnara
itrujnara reviewed May 7, 2024
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subworkflows/local/get_orthologs.nf Outdated
@@ -131,20 +131,22 @@ workflow GET_ORTHOLOGS {
ch_versions
.mix(FETCH_INSPECTOR_GROUP_ONLINE.out.versions)
.set { ch_versions }
// TODO check that this is correct
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I believe this if is not needed, this is inside the use_all block, which uses all databases no matter the other parameters (a concept from Cedric). In this case, local_databases controls preference for local databases, rather than using only local ones. This is a bit complicated, but I believe it is necessary.

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Reverted

itrujnara
itrujnara reviewed May 7, 2024
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Thanks for the tweaks Jose. I have one remark about EggNOG, the rest looks fully reasonable. Do we want review from another person before accepting this PR?

@JoseEspinosa JoseEspinosa marked this pull request as ready for review May 7, 2024 16:49
itrujnara
itrujnara approved these changes May 8, 2024
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LGTM now

@itrujnara itrujnara merged commit bf893c4 into nf-core:dev May 8, 2024
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@itrujnara itrujnara itrujnara approved these changes

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@JoseEspinosa @itrujnara