feat: Common contribution guidelines - #154
Open
fellen31 wants to merge 15 commits into
Open
Conversation
PR checklist
See Contributing Guidelines for more details on how to contribute according to pipeline conventions. |
|
fellen31
commented
Jul 1, 2026
fellen31
marked this pull request as ready for review
July 1, 2026 13:43
fellen31
marked this pull request as draft
July 2, 2026 07:54
| multiqc_config: false | ||
| nextflow_config: | ||
| - params.input | ||
| template_strings: |
Contributor
There was a problem hiding this comment.
Could you explain what these template_strings are about? Or point me to the nf-core documentation because I couldn't find it... 🤔
Contributor
Author
There was a problem hiding this comment.
Since nf-core also use jinja for their template string, this linting check is there to make sure that there are no template strings left in the template (which could mean a broken template): https://nf-co.re/tools/docs/4.0.2/pipeline_lint_tests/template_strings.
Contributor
There was a problem hiding this comment.
Ah! And the README of genomic-medicine-sweden/nf-dev-guidelines already includes information on this too - great!!!
However, I don't see any such strings in the config file? Am I missing something? 🤔
Contributor
Author
There was a problem hiding this comment.
No, it was probably an artifact from an older version. There should be no template strings in the config.
Co-authored-by: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Co-authored-by: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Co-authored-by: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
fellen31
marked this pull request as ready for review
July 2, 2026 13:50
fellen31
pushed a commit
to genomic-medicine-sweden/nf-dev-guidelines
that referenced
this pull request
Jul 9, 2026
As discussed in Clinical-Genomics/oncorefiner#154 (comment), it is more intuitive if the config file is named `contribution-guidelines-config.yaml`.
| nextflow_config: | ||
| - params.input | ||
| template_strings: | ||
| - assets/nf-dev-guidelines.yaml |
Removed template_strings configuration from nextflow_config.
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
2 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 https://github.com/Clinical-Genomics/MTP-oncoflow/issues/85. The PR that will be generated: #155.
Added
Changed
.nf-core.ymlto allow for template strings in contribution guidelines sync workflow