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Merged
merged 48 commits into from
Jun 30, 2025
Merged

Add opt-in feature gpu #3562

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1440906
optin
ningyuxin1999 May 10, 2025
087c2f0
[automated] Update CHANGELOG.md
nf-core-bot May 10, 2025
e877b6c
Merge branch 'dev' into optin
ningyuxin1999 Jun 2, 2025
e2001cb
Merge branch 'dev' into optin
ningyuxin1999 Jun 2, 2025
5f9a01c
restructured the features, add GPU and downstream sample sheet, turne…
ningyuxin1999 Jun 2, 2025
b760fd3
Merge branch 'dev' into optin
ningyuxin1999 Jun 2, 2025
19b646f
Merge branch 'dev' into optin
ningyuxin1999 Jun 2, 2025
5e54606
Merge pull request #3602 from nf-core/dev
mashehu Jun 2, 2025
2994d22
Merge branch 'dev' into optin
mashehu Jun 3, 2025
edc124f
all features are on except for gpu
ningyuxin1999 Jun 3, 2025
e33055b
update snapshot
ningyuxin1999 Jun 6, 2025
66568a7
Merge branch 'dev' into optin
ningyuxin1999 Jun 9, 2025
861016f
Merge branch 'dev' into optin
ningyuxin1999 Jun 10, 2025
410da4d
Merge branch 'dev' into optin
ningyuxin1999 Jun 11, 2025
bd4f69d
Merge branch 'nf-core:main' into optin
ningyuxin1999 Jun 11, 2025
7a0dd89
Merge branch 'dev' into optin
ningyuxin1999 Jun 16, 2025
3287df5
Merge branch 'dev' into optin
ningyuxin1999 Jun 17, 2025
393dcf2
test snaps
ningyuxin1999 Jun 17, 2025
08366c9
Merge branch 'dev' into optin
ningyuxin1999 Jun 23, 2025
6e177e7
Merge branch 'dev' into optin
mashehu Jun 24, 2025
d34f214
Merge branch 'dev' into optin
ningyuxin1999 Jun 24, 2025
39546b6
remove downstream_samplesheet feature
mirpedrol Jun 25, 2025
5039d8c
remove unwanted log.txt
mirpedrol Jun 25, 2025
d08e3f2
use feature sections to classify the switches
mirpedrol Jun 25, 2025
0cf08ba
update yq command to read new template_features.yml structure
mirpedrol Jun 25, 2025
c5cefe5
update tests accessing template_features.yml
mirpedrol Jun 25, 2025
f40bb9e
fix yq command
mirpedrol Jun 25, 2025
fa45b84
fix getting skip paths
mirpedrol Jun 25, 2025
56287e8
fix lint_config
mirpedrol Jun 25, 2025
db16ba9
fix linting config again
mirpedrol Jun 25, 2025
96ad114
fix nf-test linting when nf-test is skipped
mirpedrol Jun 26, 2025
4a85405
fix nf-test snapshots for non nf-core pipelines
mirpedrol Jun 26, 2025
157ed09
more test snapshots fixes
mirpedrol Jun 26, 2025
0aafacf
last pipeline test snapshot fixes
mirpedrol Jun 26, 2025
f6c1395
update pytest snapshots
mirpedrol Jun 26, 2025
6714e08
update pytest snapshots
mirpedrol Jun 26, 2025
6135c45
fix test_customisation_help snapshot
mirpedrol Jun 26, 2025
e3b1c72
fix toggle_all binding
mirpedrol Jun 26, 2025
a4457f9
Update nf_core/pipelines/create/create.py
ningyuxin1999 Jun 26, 2025
21dacd4
formatting
ningyuxin1999 Jun 26, 2025
6cac3f2
debug
ningyuxin1999 Jun 26, 2025
a6232f2
debug
ningyuxin1999 Jun 26, 2025
a4a1381
Update nf_core/pipelines/create/custompipeline.py
ningyuxin1999 Jun 26, 2025
7560674
pre-commit
ningyuxin1999 Jun 26, 2025
3f0c061
[automated] Update Textual snapshots
nf-core-bot Jun 26, 2025
df1ce2d
snapshotupdate
ningyuxin1999 Jun 27, 2025
bfafb49
[automated] Update Textual snapshots
nf-core-bot Jun 27, 2025
42b5524
snapshot update from gitpod
ningyuxin1999 Jun 30, 2025
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9 changes: 8 additions & 1 deletion .github/snapshots/adaptivecard.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/ci.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/citations.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/code_linters.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/codespaces.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/documentation.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/email.nf.test.snap
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6 changes: 5 additions & 1 deletion .github/snapshots/fastqc.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/github_badges.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/gitpod.nf.test.snap
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116 changes: 116 additions & 0 deletions .github/snapshots/gpu.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/igenomes.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/license.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/nf_core_configs.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/nf_schema.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/rocrate.nf.test.snap
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9 changes: 8 additions & 1 deletion .github/snapshots/seqera_platform.nf.test.snap
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