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Reorganise local modules into subfolder/main.nf for consistency #1083

Merged
merged 7 commits into from
Oct 11, 2023
Merged

Reorganise local modules into subfolder/main.nf for consistency #1083

merged 7 commits into from
Oct 11, 2023

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adamrtalbot
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@adamrtalbot adamrtalbot commented Oct 5, 2023 •
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Reorganises local modules and subworkflows into subfolder/main.nf

Changes:

  • Moves every local module and subworkflow into a named subfolder
  • Each module and subworkflow uses a main.nf file
  • Improves consistency between local and nf-core
  • Should make it easier to create nf-tests

Fixes #1080

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/rnaseq 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>).
  • 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).

@adamrtalbot
Reorganises local modules into subfolder/main.nf
3112795 
Changes:
 - Moves every local module into a named subfolder
 - Each module uses a main.nf file
 - Improves consistency between modules (local and nf-core)
 - Should make it easier to create nf-tests

Fixes #1080

- [ ] 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](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir \u003cOUTDIR\u003e`).
- [ ] 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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github-actions bot commented Oct 5, 2023

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 @adamrtalbot,

It looks like this pull-request is has been made against the nf-core/rnaseq 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/rnaseq 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!

@adamrtalbot adamrtalbot changed the base branch from master to dev October 5, 2023 11:07
@adamrtalbot
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@nf-core-bot fix linting

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github-actions bot commented Oct 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41afa96

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 19:31:54

@adamrtalbot
Changes:
966e19c 
 - Moves every local subworkflow into a named subfolder
 - Each workflow uses a main.nf file
 - Improves consistency between subworkflows (local and nf-core)
 - Should make it easier to create nf-tests
@adamrtalbot
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Linting fixes are in #1088

drpatelh
drpatelh reviewed Oct 11, 2023
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drpatelh
drpatelh reviewed Oct 11, 2023
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drpatelh
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drpatelh
drpatelh approved these changes Oct 11, 2023
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🏅

@drpatelh drpatelh merged commit 1ff095a into dev Oct 11, 2023
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@drpatelh drpatelh mentioned this pull request Oct 15, 2023
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@drpatelh drpatelh deleted the reorg_local_modules_to_subfolders branch November 21, 2023 09:44
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Move local modules and subworkflows to tool/main.nf
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