Add opt-in feature `gpu` #3562

ningyuxin1999 · 2025-05-10T20:57:13Z

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

nf_core/utils.py

…d off features as defaut

mashehu · 2025-06-03T11:59:59Z

@nf-core-bot changelog

ewels · 2025-06-03T12:51:33Z

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

Left some comments for tracking, I will tackle them 👍

log.txt

.github/snapshots/downstream_samplesheet.nf.test.snap

nf_core/pipelines/create/custompipeline.py

nf_core/pipelines/create/template_features.yml

codecov · 2025-06-26T10:02:43Z

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

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

nf_core/pipeline-template/tests/default.nf.test

nf_core/pipelines/create/create.py

nf_core/pipelines/create/custompipeline.py

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

ningyuxin1999 · 2025-06-26T14:22:07Z

@nf-core-bot update snapshots

ningyuxin1999 · 2025-06-27T13:37:01Z

@nf-core-bot update snapshots

ningyuxin1999 and others added 2 commits May 10, 2025 22:50

optin

1440906

[automated] Update CHANGELOG.md

087c2f0

ningyuxin1999 requested a review from mirpedrol May 12, 2025 11:59

mirpedrol reviewed May 13, 2025

View reviewed changes

nf_core/utils.py Outdated Show resolved Hide resolved

ningyuxin1999 and others added 5 commits June 2, 2025 10:58

Merge branch 'dev' into optin

e877b6c

Merge branch 'dev' into optin

e2001cb

restructured the features, add GPU and downstream sample sheet, turne…

5f9a01c

…d off features as defaut

Merge branch 'dev' into optin

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Merge branch 'dev' into optin

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ningyuxin1999 marked this pull request as ready for review June 2, 2025 13:32

Merge pull request nf-core#3602 from nf-core/dev

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ningyuxin1999 requested a review from mashehu June 2, 2025 14:53

Merge branch 'dev' into optin

2994d22

ewels linked an issue Jun 3, 2025 that may be closed by this pull request

Add opt-in option to template features #3315

Closed

3 tasks

ningyuxin1999 and others added 12 commits June 3, 2025 16:42

all features are on except for gpu

edc124f

update snapshot

e33055b

Merge branch 'dev' into optin

66568a7

Merge branch 'dev' into optin

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Merge branch 'dev' into optin

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Merge branch 'nf-core:main' into optin

bd4f69d

Merge branch 'dev' into optin

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Merge branch 'dev' into optin

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test snaps

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Merge branch 'dev' into optin

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Merge branch 'dev' into optin

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Merge branch 'dev' into optin

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mirpedrol reviewed Jun 25, 2025

View reviewed changes

remove downstream_samplesheet feature

39546b6

mirpedrol added 11 commits June 25, 2025 16:10

fix getting skip paths

fa45b84

fix lint_config

56287e8

fix linting config again

db16ba9

fix nf-test linting when nf-test is skipped

96ad114

fix nf-test snapshots for non nf-core pipelines

4a85405

more test snapshots fixes

157ed09

last pipeline test snapshot fixes

0aafacf

update pytest snapshots

f6c1395

update pytest snapshots

6714e08

fix test_customisation_help snapshot

6135c45

fix toggle_all binding

e3b1c72

mirpedrol approved these changes Jun 26, 2025

View reviewed changes

mashehu approved these changes Jun 26, 2025

View reviewed changes

ningyuxin1999 and others added 6 commits June 26, 2025 14:22

Update nf_core/pipelines/create/create.py

a4457f9

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

formatting

21dacd4

debug

6cac3f2

debug

a6232f2

Update nf_core/pipelines/create/custompipeline.py

a4a1381

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

pre-commit

7560674

nf-core-bot and others added 2 commits June 26, 2025 14:23

[automated] Update Textual snapshots

3f0c061

snapshotupdate

df1ce2d

nf-core-bot and others added 2 commits June 27, 2025 13:38

[automated] Update Textual snapshots

bfafb49

snapshot update from gitpod

42b5524

ningyuxin1999 enabled auto-merge (squash) June 30, 2025 11:49

ningyuxin1999 merged commit c18c21d into nf-core:dev Jun 30, 2025
98 checks passed

ningyuxin1999 deleted the optin branch June 30, 2025 12:13

mirpedrol mentioned this pull request Jun 30, 2025

create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools #3261

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Add opt-in feature `gpu` #3562

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ningyuxin1999 commented May 10, 2025 •

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ningyuxin1999 commented Jun 26, 2025

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Add opt-in feature gpu #3562

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ningyuxin1999 commented Jun 26, 2025

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