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Add more resource usage guidance docs#1055

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jfy133 wants to merge 7 commits into
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resource-guidance
Open

Add more resource usage guidance docs#1055
jfy133 wants to merge 7 commits into
devfrom
resource-guidance

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@jfy133

@jfy133 jfy133 commented Jun 23, 2026

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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

jfy133 added 2 commits June 23, 2026 15:02
@jfy133
Expand resource usage guidance in documentation
23f3ecb 
Added detailed resource usage guidance for nf-core/mag pipeline, including default resource requests for each module.
@jfy133
Add link to Resource guidance in usage.md
a705b32 
Updated usage documentation to include new resource guidance link.
@jfy133 jfy133 marked this pull request as draft June 23, 2026 13:03
@github-actions

github-actions Bot commented Jun 23, 2026 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit e60aa7d

+| ✅ 391 tests passed       |+
#| ❔   1 tests were ignored |#
Details

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-25 06:41:47

@jfy133 jfy133 marked this pull request as ready for review June 23, 2026 15:46
dialvarezs
dialvarezs reviewed Jun 23, 2026
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@dialvarezs dialvarezs left a comment

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I will leave this on stand-by until I finish to run the benchmarks to see if something needs some tuning.

Comment thread nextflow.config Outdated
@jfy133 @dialvarezs
Update nextflow.config
5f8ec6c 
Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com>
d4straub
d4straub reviewed Jun 24, 2026
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Thats fine and might give a first impression how much resources might be needed, I think.
I am a little concerned that this will be forgotten to be updated when resources/configs are updated where it matters. imho its usually not good to have data/settings duplicated. But I guess here thats not really possible to avoid.

@jfy133

jfy133 commented Jun 24, 2026 •
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Thats fine and might give a first impression how much resources might be needed, I think. I am a little concerned that this will be forgotten to be updated when resources/configs are updated where it matters. imho its usually not good to have data/settings duplicated. But I guess here thats not really possible to avoid.

Yes, agreed. That's why I added a comment, but I've also made a suggestion people seem interested in to actually add this via a nf-core tools lint to have a table and update it as necessary, feel free to add support: https://nfcore.slack.com/archives/CE5LG7WMB/p1782229336968889

Or now on github issue: nf-core/tools#4345

@jfy133 jfy133 mentioned this pull request Jun 24, 2026
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@dialvarezs

dialvarezs commented Jun 24, 2026

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We can add a note to CONTRIBUTING.md for now.

erikrikarddaniel
erikrikarddaniel approved these changes Jun 24, 2026
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Good addition! Just a few comments.

Comment thread docs/usage/resource_guidance.md
Comment thread docs/usage/resource_guidance.md Outdated
Comment thread docs/usage/resource_guidance.md Outdated
Comment thread docs/usage/resource_guidance.md

@erikrikarddaniel erikrikarddaniel Jun 24, 2026

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The long table might become a maintenance headache, but it will be useful I believe. In a better world, this would be generated by nf-core/tools by inspection of module code perhaps?

@jfy133 jfy133 Jun 25, 2026

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Yes, I've made an issue proposing this: nf-core/tools#4345, if you want to add support to it :)

@jfy133 @erikrikarddaniel
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11ae462 
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
jfy133
jfy133 commented Jun 25, 2026
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Comment thread docs/usage/resource_guidance.md
Comment thread docs/usage/resource_guidance.md Outdated
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes
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