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Add topics to the template + update linting #3779

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Merged
nvnieuwk merged 34 commits into from
Oct 29, 2025
Merged

Add topics to the template + update linting #3779

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8fc05a5
update module and subworkflow template
nvnieuwk Sep 26, 2025
de4908f
[automated] Update CHANGELOG.md
nf-core-bot Sep 26, 2025
4d94180
Merge branch 'dev' into feat/topics
nvnieuwk Sep 29, 2025
c48f7ac
also emit versions
nvnieuwk Sep 29, 2025
b534065
Merge branch 'dev' into feat/topics
nvnieuwk Sep 30, 2025
62ea7f0
add main.nf linting for topics
nvnieuwk Sep 30, 2025
e490c68
Update modules lint --fix to work with eval
nvnieuwk Sep 30, 2025
5f1af90
Update nf_core/module-template/main.nf
nvnieuwk Oct 1, 2025
1c6f6c9
versions emit should now contain the tool name
nvnieuwk Oct 1, 2025
a749470
Merge branch 'feat/topics' of github.com:nvnieuwk/tools into feat/topics
nvnieuwk Oct 1, 2025
6cb96ee
linting fixes for new versions topics
nvnieuwk Oct 1, 2025
a4d8aac
Merge branch 'dev' into feat/topics
nvnieuwk Oct 8, 2025
5a31432
add topic handling to the main workflow
nvnieuwk Oct 8, 2025
0e726e1
pre-commit
nvnieuwk Oct 8, 2025
249c8eb
add versions file as valid topic output + fix meta yaml template
nvnieuwk Oct 9, 2025
6b02333
update meta yaml versions output on module create
nvnieuwk Oct 9, 2025
f9f42a1
Merge branch 'dev' into feat/topics
nvnieuwk Oct 9, 2025
3095597
pre-commit
nvnieuwk Oct 9, 2025
0eea1b4
pre-commit
nvnieuwk Oct 9, 2025
2d49346
sort versions output
nvnieuwk Oct 13, 2025
c7be4d7
try to add versions on module creation
nvnieuwk Oct 13, 2025
5e1928d
update topics structure + added a check for empty input and output
nvnieuwk Oct 14, 2025
53f356c
Merge branch 'dev' into feat/topics
nvnieuwk Oct 14, 2025
b150244
fix wrongly resolved merge conflict
nvnieuwk Oct 14, 2025
7c954d6
fix module create tests + pre-commit
nvnieuwk Oct 14, 2025
fbe8f63
fix usage of versions string
nvnieuwk Oct 16, 2025
58d4ba7
Merge branch 'dev' into feat/topics
nvnieuwk Oct 16, 2025
914ca61
Merge branch 'dev' into feat/topics
nvnieuwk Oct 28, 2025
93f8cc1
re-allow versions yaml in linting
nvnieuwk Oct 28, 2025
31ae184
add topic linting check
nvnieuwk Oct 28, 2025
efd1176
fix review comments
nvnieuwk Oct 29, 2025
8ffc35f
Merge branch 'dev' into feat/topics
nvnieuwk Oct 29, 2025
4500ae5
fix linting
nvnieuwk Oct 29, 2025
5e39aa4
Merge branch 'feat/topics' of github.com:nvnieuwk/tools into feat/topics
nvnieuwk Oct 29, 2025
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[automated] Update CHANGELOG.md
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@nf-core-bot
nf-core-bot committed Sep 26, 2025
commit de4908fb33669efba4dfe092d1f0aa450848e53b
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@
- ignore files in gitignore also for pipeline_if_empty_null lint test ([#3722](https://github.com/nf-core/tools/pull/3722))
- do not check pytest_modules.yml file, deprecating ([#3748](https://github.com/nf-core/tools/pull/3748))
- Use the org from the .nf-core.yml when linting manifest name and homePage. ([#3767](https://github.com/nf-core/tools/pull/3767))
- Add `topics` to the template + update linting ([#3779](https://github.com/nf-core/tools/pull/3779))

### Modules

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