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Add opt-in feature gpu#3562

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ningyuxin1999 merged 48 commits intonf-core:devfrom
ningyuxin1999:optin
Jun 30, 2025
Merged

Add opt-in feature gpu#3562
ningyuxin1999 merged 48 commits intonf-core:devfrom
ningyuxin1999:optin

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@ningyuxin1999 ningyuxin1999 commented May 10, 2025 •
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Add opt-in option to template features (issue #3315)

Turned off the switch for gpu in the textual app by default.

  • Organising the switches into sections, with a specific section for opt-in features.

Added gpu to the template nf-core.yml.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@ningyuxin1999 ningyuxin1999 requested a review from mirpedrol May 12, 2025 11:59
mirpedrol
mirpedrol reviewed May 13, 2025
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@ningyuxin1999 ningyuxin1999 marked this pull request as ready for review June 2, 2025 13:32
@ningyuxin1999 ningyuxin1999 requested a review from mashehu June 2, 2025 14:53
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mashehu commented Jun 3, 2025

@nf-core-bot changelog

@ewels ewels linked an issue Jun 3, 2025 that may be closed by this pull request
Add opt-in option to template features #3315
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ewels commented Jun 3, 2025 •
edited by ningyuxin1999
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Comments from @mashehu :

  • Do we want to add grouping in the user interface at this stage, to avoid having a long list of options?
    • It's already grouped in the code.
  • Didn't see the GPU thing in the list? Features list?
  • All toggles are off, they should be on, also for nf-core (or decide what the default values should be)
    • Shouldn't be everything off by default, only gpu

mirpedrol
mirpedrol reviewed Jun 25, 2025
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Left some comments for tracking, I will tackle them 👍

Comment thread log.txt Outdated
Comment thread .github/snapshots/downstream_samplesheet.nf.test.snap Outdated
Comment thread nf_core/pipelines/create/custompipeline.py
Comment thread nf_core/pipelines/create/template_features.yml Outdated
Comment thread nf_core/pipelines/create/template_features.yml Outdated
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codecov Bot commented Jun 26, 2025 •
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Codecov Report

Attention: Patch coverage is 95.52239% with 3 lines in your changes missing coverage. Please review.

Project coverage is 76.77%. Comparing base (7e944da) to head (42b5524).
Report is 22 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/pipelines/create/__init__.py 0.00% 1 Missing ⚠️
nf_core/pipelines/create/custompipeline.py 90.90% 1 Missing ⚠️
nf_core/pipelines/lint/nf_test_content.py 96.42% 1 Missing ⚠️

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mirpedrol
mirpedrol approved these changes Jun 26, 2025
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Tests are fixed! 🥳
It would be good if someone else reviews it, since both @ningyuxin1999 and me made changes. Thanks!

mashehu
mashehu approved these changes Jun 26, 2025
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Comment thread nf_core/pipeline-template/tests/default.nf.test
Comment thread nf_core/pipelines/create/create.py Outdated
Comment thread nf_core/pipelines/create/create.py Outdated
Comment thread nf_core/pipelines/create/custompipeline.py Outdated
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ningyuxin1999 commented Jun 26, 2025

@nf-core-bot update snapshots

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ningyuxin1999 commented Jun 27, 2025

@nf-core-bot update snapshots

@ningyuxin1999 ningyuxin1999 enabled auto-merge (squash) June 30, 2025 11:49
@ningyuxin1999 ningyuxin1999 merged commit c18c21d into nf-core:dev Jun 30, 2025
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@ningyuxin1999 ningyuxin1999 deleted the optin branch June 30, 2025 12:13
@mirpedrol mirpedrol mentioned this pull request Jun 30, 2025
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@edmundmiller edmundmiller mentioned this pull request Jul 14, 2025
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Add opt-in option to template features

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