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docs: Update documentation#48

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beatrizsavinhas wants to merge 74 commits intodevfrom
28-update-documentation
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docs: Update documentation#48
beatrizsavinhas wants to merge 74 commits intodevfrom
28-update-documentation

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@beatrizsavinhas beatrizsavinhas commented Mar 12, 2026 •
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Closes #28.

Changed

  • Added .github/CONTRIBUTING.md to the list of files for lint ignore since it no longer follows the nf-core template.
  • Added link to Contributing Guidelines documentation to ISSUE_TEMPLATE/config.yml.

Fixed

  • Updated template description in .nf-core.yml.
  • Updated parameters.md by running pre-commit.
  • Fix formatting and typos and added missing information in CHANGELOG.md.
  • Updated .github/CONTRIBUTING.md:
    • Moved to docs directory to make the file easier to find.
    • Added general and development instructions:
      • How to install dependencies for development.
      • How to update the nf-core tools template.
      • Relevant guidelines based on nf-core/raredisease.
      • Other miscellaneous guidelines.
    • Added information on PR conventions and review process.
  • Updated README.md:
    • Added placeholder logo.
    • Filled in introduction section.
    • Added contributors.
    • Updated Usage section.
  • Updated CITATIONS.md.
  • Updated docs/usage.md. Input information will be updated when the input file structure is decided.
  • Updated docs/output.md with an example. To be expanded when output file structure is decided.
  • Updated pr_checklist_comment_body.md to reflect updated contributing guidelines.

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github-actions bot commented Mar 12, 2026 •
edited by beatrizsavinhas
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PR checklist

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

@beatrizsavinhas beatrizsavinhas changed the title Update documentation docs: Update documentation Mar 12, 2026
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github-actions bot commented Mar 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 09ee60d

+| ✅ 180 tests passed       |+
#| ❔  16 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  15 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: 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: 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 nextflow.config: Specify any additional parameters here
  • 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 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.
  • local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-04-13 12:59:13

beatrizsavinhas
beatrizsavinhas commented Mar 16, 2026
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beatrizsavinhas
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beatrizsavinhas
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README.md
<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use Clinical-Genomics/oncorefiner for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->

<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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@beatrizsavinhas beatrizsavinhas Mar 16, 2026 •
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Added to CITATIONS.md which is mentioned in the next line.
If we use additional data in the pipeline in the future, we should document that here.

beatrizsavinhas
beatrizsavinhas commented Mar 16, 2026
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beatrizsavinhas
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beatrizsavinhas and others added 2 commits April 7, 2026 11:40
@beatrizsavinhas @fevac
Update README.md
adad278 
Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com>
@beatrizsavinhas
Update README.md.
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beatrizsavinhas
beatrizsavinhas commented Apr 7, 2026
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subworkflows/local/utils_nfcore_oncorefiner_pipeline/main.nf
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@beatrizsavinhas beatrizsavinhas Apr 7, 2026

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I think this logic with overriding citations and bibliography is not the best... Do you have an idea for a cleaner solution?

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Would this be updated with new TEMPLATE releases? I do agree that its not a good solution, but if its from the template, idk if we can do much?

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@beatrizsavinhas beatrizsavinhas Apr 13, 2026

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I don't think so since the template simply contains a section that should be modified by the user.
What I was referring to here is about the overriding of the citations and bibliography variables in the code I wrote!

@beatrizsavinhas beatrizsavinhas marked this pull request as ready for review April 7, 2026 11:23
@beatrizsavinhas beatrizsavinhas requested a review from a team as a code owner April 7, 2026 11:23
@beatrizsavinhas beatrizsavinhas marked this pull request as draft April 7, 2026 11:23
@beatrizsavinhas beatrizsavinhas marked this pull request as ready for review April 13, 2026 07:09
mathiasbio
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docs/CONTRIBUTING.md

### Channels

- **Conditional channels**: always initialize to `channel.empty()` before any `if` block that may or may not assign them. Never leave a channel potentially undefined.
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@mathiasbio mathiasbio Apr 13, 2026 •
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Does this need to be updated now? 🤔 I mean regarding what you were saying at the meeting about if statements for channels always being true

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@beatrizsavinhas beatrizsavinhas Apr 13, 2026 •
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No, this is just referring to if statements that determine if the channel is populated or not, for example:

ch_example = channel.empty()

if (<condition_to_populate_the_channel>):
	ch_example = channel.of(<something>)

So that if down the line this channel is used for something, you are always sure the channel is at least an empty channel (never undefined).

What we discussed in the meeting is that if statements like if (ch_example) always return true because even if the channel is empty, it exists.

Hope that clears it out for you!

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subworkflows/local/utils_nfcore_oncorefiner_pipeline/main.nf
Comment on lines +221 to +225
def vcfanno = "<li>Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5. PMID: 27250555; PMCID: PMC4888505.</li>"
def bcftools_view = "<li>Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590845; PMCID: PMC7898596.</li>"
def ensemblvep_vep = "<li>McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PMID: 27268795; PMCID: PMC4893825.</li>"
def svdb = "<li>svdb. https://github.com/J35P312/svdb.</li>"
def multiqc = "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
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Interesting that this text is here! I would have thought it would be referenced maybe from some type of constants file. But I assume this is the best practices!

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Yeah, I agree that something like a constants file or, even better, parsing from CITATIONS.md would be better! But for now it seems like this is the idea in the updated nf-core template.

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This looks good from my point of view! 🌟 Awesome job! I will approve! But with a disclaimer and full understanding that you might want to wait for someone with more experience : )

kristinebilgrav
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docs/CONTRIBUTING.md
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test in the `tests` directory.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
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We already have a MultiQC module, so the use case of latter part of this is a little confusing to me?

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@beatrizsavinhas beatrizsavinhas Apr 13, 2026 •
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This sentence was taken from the original template and I believe it is referring to these MultiQC modules: https://docs.seqera.io/multiqc/modules/.

kristinebilgrav
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docs/CONTRIBUTING.md Outdated

### Configuration

- Process-level options go in `conf/modules/<subworkflow_name>.config`, not inline in the subworkflow `.nf` file.
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@kristinebilgrav kristinebilgrav Apr 13, 2026 •
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As of now, process-level options are added to conf/modules.config right? I do like the idea of having it like this instead though (maybe in conf/subworkflows/<subworkflow_name>.config instead but still)! (If I understand this correctly?). Should we create an issue to convert it to this?

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Ah good catch! We have recently updated to using conf/subworkflows/<subworkflow_name>.config so I'll change these instructions.

About the issue to refactor the current code to adhere to this logic, we will already fix that for the new subworkflows in https://github.com/Clinical-Genomics/CancerBioInfo/issues/104 and the only one that is left is PREPARE_REFERENCES. Since you will work on this subworkflow soon, could you fix that config too?

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Nice!

Perfect! Yes, I can do that!

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Had a few comments, but otherwise looks great - well done! 🌟

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Update documentation

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