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docs: Update CONTRIBUTING.md from nf-dev-guidelines - #155

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docs: Update CONTRIBUTING.md from nf-dev-guidelines#155
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@nf-guidelines-sync-bot nf-guidelines-sync-bot Bot commented Jul 1, 2026

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Auto-generated from nf-dev-guidelines.

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nf-guidelines-sync-bot Bot requested a review from a team as a code owner July 1, 2026 12:58
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PR checklist

  • Fill in description of the PR and link to any relevant issues.
  • If you've fixed a bug, added a subworkflow or any other code that should be tested, add tests!
  • If you've added a new tool, update citations according to the instructions under Adding Citations.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including authors/contributors).

See Contributing Guidelines for more details on how to contribute according to pipeline conventions.

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github-actions Bot commented Jul 1, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 8bfccc5

+| ✅ 193 tests passed       |+
#| ❔  22 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  12 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • modules_json - Your modules.json file is outdated. It will be automatically generated by running any module command.

❗ 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: Include a figure that guides the user through the major workflow steps. Many nf-core
  • 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 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-01 13:35:44

@nf-guidelines-sync-bot nf-guidelines-sync-bot Bot changed the title Update CONTRIBUTING.md from nf-dev-guidelines docs: Update CONTRIBUTING.md from nf-dev-guidelines Jul 1, 2026
@nf-guidelines-sync-bot
nf-guidelines-sync-bot Bot force-pushed the update-contributing-guidelines branch from 58617ba to 8feaa9a Compare July 1, 2026 13:01
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md Outdated
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
Comment on lines +236 to +250
- Both `take:` and `emit:` block entries require an inline type comment. Use `name // type: [mandatory|optional] description` for `take:` and `name = value // channel: [type description]` for `emit:`. Always include the comment — never leave an entry uncommented.

```groovy
take:
ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ]
ch_reduced_penetrance // channel: [optional] [ path(penetrance) ]
val_aligner // string: [mandatory] aligner name (bwa/bwamem2/bwameme)
process_with_sort // Boolean

emit:
vcf = ch_vcf // channel: [ val(meta), path(vcf) ]
publish = ch_publish // channel: [ val(destination), val(value) ]
```

- Use `ch_* = <...>` to declare a new channel. Avoid using `.set { ch_* }`.

@fellen31 fellen31 Jul 1, 2026

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Mostly just changing location.

@nf-guidelines-sync-bot
nf-guidelines-sync-bot Bot force-pushed the update-contributing-guidelines branch from 8feaa9a to 3770e7e Compare July 1, 2026 13:13
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
Comment on lines -217 to -219
### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

@fellen31 fellen31 Jul 1, 2026

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This link is broken (#80). Hope it's okay that this section disappears.

fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
@nf-guidelines-sync-bot
nf-guidelines-sync-bot Bot force-pushed the update-contributing-guidelines branch 2 times, most recently from c2541e9 to 8bfccc5 Compare July 1, 2026 13:34
fellen31
fellen31 reviewed Jul 1, 2026
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Comment thread docs/CONTRIBUTING.md
- [Adding a new step](#adding-a-new-step)
- [Channels](#channels)
- [Naming schemes](#naming-schemes)
- [Naming conversions](#naming-conversions)

@fellen31 fellen31 Jul 1, 2026

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Previously broken in original docs, header is naming conventions.

@beatrizsavinhas beatrizsavinhas Jul 1, 2026

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Correct! I just noticed that today so it's nice that it's fixed!

@fellen31 fellen31 mentioned this pull request Jul 1, 2026
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@nf-guidelines-sync-bot
nf-guidelines-sync-bot Bot force-pushed the update-contributing-guidelines branch from 8bfccc5 to 26981cf Compare July 2, 2026 07:54
@nf-guidelines-sync-bot
nf-guidelines-sync-bot Bot force-pushed the update-contributing-guidelines branch from 26981cf to a0c7fd8 Compare July 2, 2026 12:23
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