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Add spades options #272

Merged
merged 15 commits into from
Mar 19, 2024
Merged

Add spades options #272

merged 15 commits into from
Mar 19, 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 an option for Spades that allows the user to run the tool in different flavour.
This pr address to #271 issue

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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 @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 13, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 44234ed

+| ✅ 168 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 2024-03-19 09:16:01

erikrikarddaniel
erikrikarddaniel approved these changes Mar 13, 2024
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A little mixed, this PR... ;-)
Anyway, looks good except that we might want to enumerate the possible values for --spades_flavor, see comment in the code.
This perhaps merits a 1.1 release (new functionality rather than bug fixes)?

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@danilodileo danilodileo changed the base branch from master to dev March 15, 2024 12:00
erikrikarddaniel
erikrikarddaniel approved these changes Mar 15, 2024
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Two more comments.

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erikrikarddaniel
erikrikarddaniel reviewed Mar 15, 2024
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@danilodileo danilodileo merged commit ed8cf07 into nf-core:dev Mar 19, 2024
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@danilodileo danilodileo mentioned this pull request Apr 8, 2024
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@danilodileo danilodileo deleted the add-spades-options branch April 9, 2024 08:41
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel