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testing new ci#149

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mashehu wants to merge 16 commits into
nf-core:devfrom
mashehu:update-dev
Open

testing new ci#149
mashehu wants to merge 16 commits into
nf-core:devfrom
mashehu:update-dev

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@mashehu

@mashehu mashehu commented Jun 23, 2026

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ewels and others added 2 commits June 22, 2026 12:24
@ewels @claude
Consolidate and harden PR-comment GitHub Actions workflows
f9270da 
Adds a single shared `pr-comment.yml` workflow as the only one that runs
with a write token. It is triggered via `workflow_run` after a producer
workflow completes, downloads a standard `pr-comment` artifact, and posts
the comment.

The producer workflows — `linting`, `template-version-comment`, and
`branch` — now run on `pull_request` with read-only tokens and just upload
a `pr-comment` artifact (`pr_number.txt`, `header.txt`, optional
`comment.md`). They no longer post comments directly.

Removes the now-redundant `linting_comment.yml`.

Ported from nf-core/rnaseq#1872.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ewels
Merge pull request nf-core#148 from nf-core/consolidate-pr-comment-wo…
2cbdc96 
…rkflows

Consolidate and harden PR-comment GitHub Actions workflows
@mashehu

mashehu commented Jun 23, 2026

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@nf-core-bot fix linting

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@mashehu

mashehu commented Jun 23, 2026

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@nf-core-bot fix linting

@mashehu mashehu changed the base branch from main to dev June 23, 2026 09:28
ewels and others added 3 commits June 23, 2026 11:29
@ewels @mashehu
Consolidate and harden PR-comment GitHub Actions workflows
dd61a76 
Adds a single shared `pr-comment.yml` workflow as the only one that runs
with a write token. It is triggered via `workflow_run` after a producer
workflow completes, downloads a standard `pr-comment` artifact, and posts
the comment.

The producer workflows — `linting`, `template-version-comment`, and
`branch` — now run on `pull_request` with read-only tokens and just upload
a `pr-comment` artifact (`pr_number.txt`, `header.txt`, optional
`comment.md`). They no longer post comments directly.

Removes the now-redundant `linting_comment.yml`.

Ported from nf-core/rnaseq#1872.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

# Conflicts:
#	.github/workflows/branch.yml
#	.github/workflows/linting_comment.yml
#	.github/workflows/template-version-comment.yml
@mashehu
update to 3.5.0
535eb5a 
# Conflicts:
#	.editorconfig
#	.github/workflows/ci.yml
#	.github/workflows/linting_comment.yml
#	.github/workflows/template-version-comment.yml
#	.github/workflows/template_version_comment.yml
#	.nf-core.yml
#	README.md
#	nextflow.config
#	ro-crate-metadata.json
#	subworkflows/local/utils_nfcore_testpipeline_pipeline/main.nf
@nf-core-bot @mirpedrol @mashehu
Important! Template update for nf-core/tools v4.0.0 (nf-core#146)
ca90650 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: mashehu <mashehu3@gmail.com>
@mashehu mashehu changed the base branch from dev to main June 23, 2026 10:51
ewels and others added 6 commits June 23, 2026 15:30
@ewels @claude
Fix pr-comment poster never finding the artifact body
5c94814 
`dawidd6/action-download-artifact` with a single `name:` extracts the
artifact's contents into the workspace root, so `comment.md`,
`header.txt` and `pr_number.txt` landed at `./` — not under
`pr-comment/`. The metadata step's `[ -f pr-comment/comment.md ] || exit 0`
therefore always bailed and no comment was ever posted.

Add `path: pr-comment` to the download step so the files land where the
rest of the workflow expects them.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ewels @claude
Add debug logging to pr-comment metadata step
b6c8b58 
Log the downloaded artifact contents and distinguish "no artifact" from
"artifact present but no comment body" so a future path/artifact mismatch
is visible in the run output rather than silently posting nothing.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ewels
Merge pull request nf-core#150 from nf-core/fix-pr-comment-artifact-path
6383571 
Fix PR-comment poster never posting (artifact extracted to wrong path)
@ewels @claude
Trigger CI to test pr-comment poster
79dde7d 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ewels @claude
Add CHANGELOG entry to trigger CI
cf04c78 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@mashehu
Merge branch 'main' into update-dev
581fc55
@github-actions

github-actions Bot commented Jun 23, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.1.
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 Jun 23, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c3efc5b

+| ✅ 192 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  29 tests had warnings |!
Details

❗ 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 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 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)
  • 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 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 main.nf: Remove this line if you don't need a FASTA file
  • 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 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 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 nextflow.config: Specify any additional parameters here
  • 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • container_configs - Could not generate container configuration files: Command 'nextflow inspect -format json /home/runner/work/testpipeline/testpipeline' returned non-zero error code '1':
    [red]>
    Error subworkflows/local/utils_nfcore_testpipeline_pipeline/main.nf:82:5: Incorrect number of call arguments, expected 10 but received 9
    │ 80 | command = "nextflow run ${workflow.manifest.name} -profile <docker
    │ 81 |
    │ 82 | UTILS_NFSCHEMA_PLUGIN (
    │ | ^^^^^^^^^^^^^^^^^^^^^^^
    │ 83 | workflow,
    ╰ 84 | validate_params,

ERROR ~ Script compilation failed

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File does not exist: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.1
  • Run at 2026-06-24 11:40:22

@nf-core nf-core deleted a comment from github-actions Bot Jun 23, 2026
@mashehu mashehu changed the base branch from main to dev June 23, 2026 14:02
@mashehu mashehu changed the base branch from dev to main June 23, 2026 14:02
@mashehu

mashehu commented Jun 23, 2026

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@nf-core-bot fix linting

@mashehu mashehu changed the base branch from main to dev June 23, 2026 14:39
@ewels

ewels commented Jun 23, 2026 •
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Heads up @mashehu: I pushed two trivial commits here (79dde7d and cf04c78) to re-trigger CI, but they didn't fire the pull_request workflows. GitHub only runs them when the fork owner pushes; a maintainer pushing to your fork via "allow edits" doesn't trigger them, not even as an approval-pending run. So this branch's checks need a push from you to re-run (your merge of main, 581fc55, would have).

I did verify the consolidated PR-comment workflow works by re-running the linting producer. It fired the shared poster on main and the lint/branch/template-version comments posted correctly (the pr-comment.yml path: fix plus debug logging from #150).

@mashehu mashehu mentioned this pull request Jun 23, 2026
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@mashehu @ewels @maxulysse @nf-core-bot