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Initialise testing and base template functionality #4

Merged
merged 5 commits into from
Dec 15, 2023
Merged

Initialise testing and base template functionality #4

merged 5 commits into from
Dec 15, 2023

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pinin4fjords
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No useful scientific content here at all, I'm just establishing test infra etc.

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/riboseq 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).

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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 @pinin4fjords,

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

@pinin4fjords pinin4fjords changed the base branch from master to dev December 15, 2023 13:08
@pinin4fjords pinin4fjords changed the title Readd functionality Initialise testing an base template functionality Dec 15, 2023
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github-actions bot commented Dec 15, 2023 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit c7c30d9

+| ✅ 153 tests passed       |+
!| ❗  21 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • actions_ci - '.github/workflows/ci.yml' is not triggered on expected events
  • actions_ci - '.github/workflows/ci.yml' does not check minimum NF version

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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 usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRiboseq.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-15 13:19:06

@pinin4fjords pinin4fjords changed the title Initialise testing an base template functionality Initialise testing and base template functionality Dec 15, 2023
@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit de3883b into dev Dec 15, 2023
14 of 15 checks passed
@pinin4fjords pinin4fjords deleted the readd_functionality branch December 15, 2023 13:26
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@maxulysse maxulysse maxulysse approved these changes

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@pinin4fjords @maxulysse