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Update gtdbtk classifywf so doesn't break when mashdb given #608

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merged 2 commits into from Mar 26, 2024
Merged

Update gtdbtk classifywf so doesn't break when mashdb given #608

merged 2 commits into from Mar 26, 2024

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jfy133
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@jfy133 jfy133 commented Mar 26, 2024

Closes #598

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).

@jfy133 jfy133 changed the base branch from master to dev March 26, 2024 10:36
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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!

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github-actions bot commented Mar 26, 2024 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit 6f870d9

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowMag.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-26 10:39:18

@jfy133 jfy133 requested review from maxibor and CarsonJM March 26, 2024 13:41
CarsonJM
CarsonJM approved these changes Mar 26, 2024
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@CarsonJM CarsonJM left a comment

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These changes make sense to me!

@jfy133 jfy133 merged commit 1ffa881 into dev Mar 26, 2024
14 of 15 checks passed
@jfy133 jfy133 deleted the update-gtdbtk-classifwy branch March 26, 2024 14:48
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@CarsonJM CarsonJM CarsonJM approved these changes

@maxibor maxibor Awaiting requested review from maxibor

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NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF fails when all genomes classified by ANI screening step
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@jfy133 @CarsonJM