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Add test configs for krona and concoct #591

Merged
merged 3 commits into from
Feb 16, 2024
Merged

Add test configs for krona and concoct #591

merged 3 commits into from
Feb 16, 2024

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jfy133
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@jfy133 jfy133 commented Feb 16, 2024

  • Krona is included in the base test run as it's small (not sure why it was turned off)
  • CONCOCT is it's own with as any other functionality turned offf as possible to allow completion in reasonable time

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/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev February 16, 2024 14:43
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github-actions bot commented Feb 16, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 495c719

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • 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
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-16 14:46:14

@CarsonJM CarsonJM linked an issue Feb 16, 2024 that may be closed by this pull request
CONCOCT (slow) #592
Closed
@CarsonJM CarsonJM merged commit 30bde89 into dev Feb 16, 2024
14 checks passed
@jfy133 jfy133 deleted the new-configs branch August 15, 2024 19:31
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@CarsonJM CarsonJM CarsonJM approved these changes

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CONCOCT (slow)
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@jfy133 @CarsonJM