Skip to content

Copy only files which are successfully validated - #67

Merged
delfiterradas merged 8 commits into
nf-core:devfrom
delfiterradas:only_copy_validated
Jul 29, 2026
Merged

Copy only files which are successfully validated#67
delfiterradas merged 8 commits into
nf-core:devfrom
delfiterradas:only_copy_validated

Conversation

@delfiterradas

@delfiterradas delfiterradas commented Jul 27, 2026

Copy link
Copy Markdown
Contributor

Closes #62

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/datasync branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@delfiterradas delfiterradas self-assigned this Jul 27, 2026
@nf-core-bot

nf-core-bot commented Jul 27, 2026

Copy link
Copy Markdown
Member

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 28, 2026

Copy link
Copy Markdown

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 28, 2026 •
edited
Loading

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6cb7cac

+| ✅ 203 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  22 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-29 13:20:27

nf-core-bot and others added 3 commits July 28, 2026 21:57
@nf-core-bot @delfiterradas
Remove vulnerable PR-comment artifact pattern
fe97a5c 
This pipeline's TEMPLATE branch never received the nf-core/tools 4.0.3 sync, so the patch was taken from nf-core/abotyper's TEMPLATE branch with the repository identity in branch.yml rewritten for this pipeline. That identity is the only pipeline-specific content the template renders into any of the patched workflows, so this is the same change this pipeline's own sync would have produced — but the substituted source is worth a look.
@delfiterradas
Update changelog.md
cac46dd
@delfiterradas
Update rclone_copy
6cb7cac
@delfiterradas
delfiterradas marked this pull request as ready for review July 29, 2026 13:20
@delfiterradas
delfiterradas merged commit ff96d7d into nf-core:dev Jul 29, 2026
15 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@antoniasaracco antoniasaracco antoniasaracco approved these changes

Assignees

@delfiterradas delfiterradas

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Copy only files which are successfully validated

3 participants

@delfiterradas @nf-core-bot @antoniasaracco