docs: Add developing modules tutorial#4155
Merged
Merged
Conversation
✅ Deploy Preview for nf-core-docs ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
✅ Deploy Preview for nf-core-main-site ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
Member
Author
|
@nf-core-bot fix linting |
jfy133
reviewed
Apr 20, 2026
Member
jfy133
left a comment
jfy133
left a comment
There was a problem hiding this comment.
Got side tracked and have to get kits up now, but conceptual question on first page for consideration
Member
Author
|
Also - feel free to push changes. I'm not attached to anything strongly. |
jfy133
reviewed
Apr 20, 2026
Member
jfy133
left a comment
jfy133
left a comment
There was a problem hiding this comment.
Finished up to page 3, will continue from 4 onwards when I have time
|
|
||
| The following diagram shows how these files relate to each other: | ||
|
|
||
| <img width=80% alt="Diagram showing how the execution, documentation, and testing files in an nf-core module relate to each other." src="../../../../../assets/images/tutorials/training/nf-core-module-file-relationship.png"> |
jfy133
reviewed
Apr 21, 2026
Member
jfy133
left a comment
jfy133
left a comment
There was a problem hiding this comment.
Chapter 5 review done. Continuing next time from chapter 6
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
jfy133
reviewed
Apr 22, 2026
| test("sarscov2 - fastq - bakta annotation input") | ||
| ``` | ||
|
|
||
| In the `when` block, declare each input channel using `input[index]` notation (`input[0]` for the first, `input[1]` for the second, and so on). The block accepts standard Nextflow code — channel factories, operators, and so on — as you would use in a pipeline. Make sure each `input[]` matches the channel structure of your module, including any meta map: |
Member
There was a problem hiding this comment.
Suggested change
| In the `when` block, declare each input channel using `input[index]` notation (`input[0]` for the first, `input[1]` for the second, and so on). The block accepts standard Nextflow code — channel factories, operators, and so on — as you would use in a pipeline. Make sure each `input[]` matches the channel structure of your module, including any meta map: | |
| In the `when` block, declare each input channel using `input[index]` notation (`input[0]` for the first, `input[1]` for the second, and so on). | |
| The block accepts standard Nextflow code — channel factories, operators, and so on — as you would use in a pipeline. | |
| Make sure each `input[]` matches the channel structure of your module, including any meta map: |
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Member
|
@nf-core-bot fix linting |
jfy133
reviewed
Apr 22, 2026
…re-modules/3-what-is-a-module.md
jfy133
approved these changes
Apr 22, 2026
Member
jfy133
left a comment
jfy133
left a comment
There was a problem hiding this comment.
Tahnks @christopher-hakkaart !
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Closes #4145
@netlify /docs/developing/tutorials/writing-nf-core-modules/1-introduction