Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update multiqc, fastqc, filtlong, adapterremoval, dumpsoftwareversions #425

Closed
wants to merge 1 commit into from
Closed

Update multiqc, fastqc, filtlong, adapterremoval, dumpsoftwareversions #425

wants to merge 1 commit into from

Conversation

sofstam
Copy link
Collaborator

@sofstam sofstam commented Jan 11, 2024

This PR updates the following modules:

  • multiqc
  • fastqc
  • adapterremoval
  • dumpsoftwareversions
  • filtlong

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/taxprofiler 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jan 11, 2024 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit a14a2db

+| ✅ 158 tests passed       |+
!| ❗   2 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 - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/tree/dev" target="_blank">nf-core/taxprofiler</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/dev" target="_blank">nf-core/taxprofiler</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/dev/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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 passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-11 14:07:09

@sofstam sofstam closed this Jan 11, 2024
@sofstam
Copy link
Collaborator Author

sofstam commented Jan 11, 2024

Will do the update on the merge template

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@sofstam