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Transdecoder bug #270

Merged
merged 12 commits into from
Mar 4, 2024
Merged

Transdecoder bug #270

merged 12 commits into from
Mar 4, 2024

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danilodileo
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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/metatdenovo 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).

I made a local module for transdecoder in order to solve the caching issue

@danilodileo danilodileo changed the base branch from master to dev March 4, 2024 12:53
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github-actions bot commented Mar 4, 2024

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 @danilodileo,

It looks like this pull-request is has been made against the danilodileo/metatdenovo 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 danilodileo/metatdenovo 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 4, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 071a1d6

+| ✅ 170 tests passed       |+
!| ❗   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/WorkflowMetatdenovo.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:

  • nextflow_config - Config manifest.version should end in dev: 1.0.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-04 13:55:33

erikrikarddaniel
erikrikarddaniel approved these changes Mar 4, 2024
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I think you upgraded the version too early. I think you shouldn't change version number until you make a release PR. I updated to 1.0.1 in some places, but maybe it should actually still be 1.0.1dev. It certainly shouldn't be 1.0.2.

The changes I suggested to CHANGELOG.md is what I think it should look like. I compared with Ampliseq's.

CHANGELOG.md Outdated
## v1.0.0 - [date]

Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template.
## v1.0.1 - [2024-03-04]
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I'm not sure when you put in the date here, since it depends on when we get the release PR through.

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Ok, then I change it.

assets/multiqc_config.yml Outdated Show resolved Hide resolved
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I think it would perhaps been better to remove the nf-core module, and add a new local. But the effect is the same of course.

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@danilodileo danilodileo merged commit 066f21c into nf-core:dev Mar 4, 2024
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@danilodileo danilodileo deleted the transdecoder-bug branch March 13, 2024 15:10
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@danilodileo @erikrikarddaniel