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dev -> main for 3.5.0 #3872

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@mashehu mashehu commented Nov 5, 2025

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jpfeuffer and others added 30 commits September 18, 2025 14:51
@jpfeuffer
Download pipeline with auth. GH API
ae66e2e
@jpfeuffer
remove debug
191f685
@jpfeuffer
ruff linter
eff74f4
@jpfeuffer
good old indent on empty line
dfaf3fe
@jpfeuffer
read topdir from zip for rename
9ab9642
@jpfeuffer
ruff....
bb094e2
@jpfeuffer
add a cli flag to avoid rate limit when unauthenticated
b423285
@jpfeuffer
fix test
146632f
@jpfeuffer
fix test: Remove api-download param from test dict since it's a boole…
651a0ca 
…an flag
@jpfeuffer
add testing artifacts to gitignore
592d621
@jpfeuffer
lint
e77b261
@nvnieuwk
update module and subworkflow template
8fc05a5
@nf-core-bot
[automated] Update CHANGELOG.md
de4908f
@nvnieuwk
Merge branch 'dev' into feat/topics
4d94180
@nvnieuwk
also emit versions
c48f7ac
@nvnieuwk
Merge branch 'dev' into feat/topics
b534065
@nvnieuwk
add main.nf linting for topics
62ea7f0
@nvnieuwk
Update modules lint --fix to work with eval
e490c68
@nvnieuwk @mirpedrol
Update nf_core/module-template/main.nf
5f1af90 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@nvnieuwk
versions emit should now contain the tool name
1c6f6c9
@nvnieuwk
Merge branch 'feat/topics' of github.com:nvnieuwk/tools into feat/topics
a749470
@nvnieuwk
linting fixes for new versions topics
6cb96ee
@nvnieuwk
Merge branch 'dev' into feat/topics
a4d8aac
@nvnieuwk
add topic handling to the main workflow
5a31432
@nvnieuwk
pre-commit
0e726e1
@nvnieuwk
add versions file as valid topic output + fix meta yaml template
249c8eb
@nvnieuwk
update meta yaml versions output on module create
6b02333
@nvnieuwk
Merge branch 'dev' into feat/topics
f9f42a1
@nvnieuwk
pre-commit
3095597
@nvnieuwk
pre-commit
0eea1b4
JulianFlesch and others added 30 commits November 6, 2025 14:19
@JulianFlesch
Read authentication status from gh_api
8fe0b10
@JulianFlesch
Remove Redundat downloading of workflow files in favor of single requ…
bbd9f4d 
…est with gh_api
@JulianFlesch
Merge branch 'dev' into jpfeuffer-patch-1
547b84a
@mashehu
linting: update json schema store URL
f457472 
see SchemaStore/schemastore#5106 for details
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
659c624
@mashehu
Merge branch 'dev' into jpfeuffer-patch-1
6300095
@JulianFlesch
Remove the authenticated flag. Authentication will be checked automat…
7599ad5 
…ically
@JulianFlesch
Remove duplicated code section
475f83b
@JulianFlesch
Merge branch 'jpfeuffer-patch-1' of github.com:nf-core/tools into jpf…
1b9d9b5 
…euffer-patch-1
@JulianFlesch
Fix download urls for tests that run with github auth. Adds an unauth…
21703d8 
…enticated test.
@JulianFlesch
Remove removed 'authenticated' param from test call
59053c8
@JulianFlesch
Fix test with with noauth by unsetting gh_api.auth
beef14f
@JulianFlesch
Fix typo
e54481b
@JulianFlesch
Merge pull request #3607 from nf-core/jpfeuffer-patch-1
8ff5da6 
Download pipelines with authenticated GH API calls
@renovate @nf-core-bot @mashehu
Update docker/setup-qemu-action digest to c7c5346 (#3875)
f0786c4 
* Update docker/setup-qemu-action digest to c7c5346

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@renovate @nf-core-bot
chore(deps): update python:3.14-slim docker digest to 9813eec (#3880)
c9d3b76 
* chore(deps): update python:3.14-slim docker digest to 9813eec

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
@tgelafr-pfzr @nf-core-bot @rrahn
sync: Avoid deleting files ignored by git during pipelines sync (#3847
9a0ba10 
)

Co-authored-by: Tatiana Gelaf Romer <romert01@pfizer.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: René Rahn <1529364+rrahn@users.noreply.github.com>
@renovate @mashehu
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.4
ea2e079
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
cc2f59f
@mashehu
add missing setup steps to snapshot update action
9da30b8
@mashehu
remove redundant if clause
fbae502
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
e535731
@renovate @nf-core-bot @mashehu
Update dependency textual to v6.5.0 (#3859)
7dff5ee 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mashehu
update multiqc to 1.32
8bce834
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
b81aa25
@mashehu
update snapshots
5ab6be3
@mashehu
fix sync test
c2151f1
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
d096856
@JulianFlesch @mashehu
Add Changelog entry for PR 3607
e101b4f 
# Conflicts:
#	CHANGELOG.md
@mashehu @nf-core-bot
fix syntax in dockerfile for devcontainer (#3887)
b4b6a73 
Co-authored-by: nf-core-bot <core@nf-co.re>
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