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Merged
merged 723 commits into from
Oct 15, 2025
Merged

dev > main for 3.4.0 release #3833

merged 723 commits into from
Oct 15, 2025

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JulianFlesch and others added 30 commits August 29, 2025 13:07
@JulianFlesch
fix: change from using StrEnum to Enum with 'value' accessor for comp…
ec6e0e9 
…atibility with python3.9
@JulianFlesch
add changes
3698b28
@nf-core-bot
[automated] Update CHANGELOG.md
776313b
@JulianFlesch
Update changelog entry with pr
15aeedd
@JulianFlesch
Merge pull request #3736 from JulianFlesch/fix/enum-backwards-compati…
e98ae9b 
…bility

Fix/enum backwards compatibility
@JulianFlesch
Merge branch 'dev' into issues/3466-gitpod
063ec8b
@jfy133
Add github repo description text to Mastodon post
1d3f4de
@nf-core-bot
[automated] Update CHANGELOG.md
55e408c
@jfy133
Move changelog entry to correct locoation
28b2ec3
@JulianFlesch
Merge branch 'issues/3466-gitpod' of github.com:JulianFlesch/nf-core-…
73bd04b 
…tools into issues/3466-gitpod
@JulianFlesch
fix tests: Update snapshots
717fd8e
@JulianFlesch
impr: Cleanup after pip and conda
fce08cf
@JulianFlesch
impr: Move nf-test and nextflow install to Dockerfile to reduce their…
04c14dd 
… size
@JulianFlesch
impr: Add two-stage build to only keep essential files
5fb202d
@JulianFlesch
fix typo: remove duplicate line
86b1976
@JulianFlesch
impr: Move apptainer install to Dockerfile to improve container size
b4335b2
@JulianFlesch
cleanup: remove unused features and update comments
6c1596c
@JulianFlesch
impr: Use more lean base image for final stage.
285a2a1
@nvnieuwk
Bump nf-schema to 2.5.0 and update help message creation
1c939e9
@nvnieuwk
update changelog
ec2ba45
@nvnieuwk
add PR number to changelog
c915b16
@nvnieuwk
fixes to template logic
bbb041a
@nvnieuwk
bump nextflow to 25.04.0
9029471
@nvnieuwk
also bump CI nextflow version
e9e5cdb
@nvnieuwk @mirpedrol
Apply suggestions from code review
ec86cf3 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@nvnieuwk
prevent summary log duplication
0c803f8
@nvnieuwk
Merge branch 'bump/nf-schema-2.5.0' of github.com:nvnieuwk/tools into…
b172dec 
… bump/nf-schema-2.5.0
@JulianFlesch
Merge pull request #3569 from JulianFlesch/issues/3466-gitpod
78b790e 
Issues/3466 Move away from Gitpod
@JulianFlesch
impr: Add hostRequirements to run with 4CPUs and 16GB ram by default …
0cb2928 
…(available in free tier)
@nf-core-bot
[automated] Update CHANGELOG.md
4f71d25
mashehu and others added 21 commits October 14, 2025 16:28
@mashehu
template: fix launch action
3f09a86
@nf-core-bot
[automated] Update CHANGELOG.md
6afd4a9
@mashehu @mirpedrol
Update CHANGELOG.md
e2413b8 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@mashehu
Merge pull request #3827 from mashehu/fix-launch-action
15f5bfb
@mashehu
mock correct command in cache test
1ce7a5a
@mirpedrol
Merge branch 'dev' into update-template-modules
09f3ac4
@mirpedrol
Merge pull request #3826 from mirpedrol/update-template-modules
a5411fa 
update pipeline template subworkflows
@mashehu
pipelines bump-version: fix indentation for list in dumped .nf-core.yml
dfe5fcf
@mashehu
add test
d2faf1c
@mashehu
fix path
5fc6e77
@nf-core-bot
[automated] Update CHANGELOG.md
e73032f
@mashehu
remove ternary operators from container lines
10bd3bc
@nf-core-bot
[automated] Update CHANGELOG.md
245bbdc
@mirpedrol
Merge pull request #3830 from mashehu/fix-ternary-containter-linting
813dbf2 
fix ternary container linting
@mirpedrol
Revert "Add .nf-test folder to prettierignore list"
4abeb06
@nf-core-bot
[automated] Update CHANGELOG.md
ad09541
@mirpedrol @mashehu
Update CHANGELOG.md
1793280 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@mirpedrol
Merge pull request #3831 from nf-core/revert-3625-prettierignore-nftest
1034e3c 
Revert "Add .nf-test folder to prettierignore list"
@mashehu
Merge pull request #3829 from mashehu/fix-list-indendation-of-bumped-yml
e05da51
@mirpedrol
bump to 3.4.0 for release
f0ae68b
@mirpedrol
Merge pull request #3832 from mirpedrol/bump-3.4.0
b15b298 
Bump to 3.4.0 for release
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codecov bot commented Oct 15, 2025 •
edited
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Codecov Report

❌ Patch coverage is 74.47257% with 484 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.25%. Comparing base (5f61010) to head (1ebee76).
⚠️ Report is 893 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/pipelines/download/singularity.py 52.83% 191 Missing ⚠️
nf_core/pipelines/download/download.py 72.70% 95 Missing ⚠️
nf_core/pipelines/download/workflow_repo.py 67.34% 48 Missing ⚠️
nf_core/pipelines/download/docker.py 73.29% 47 Missing ⚠️
nf_core/modules/lint/main_nf.py 54.71% 24 Missing ⚠️
nf_core/pipelines/download/container_fetcher.py 88.70% 20 Missing ⚠️
nf_core/pipelines/download/utils.py 78.46% 14 Missing ⚠️
nf_core/test_datasets/list.py 25.00% 9 Missing ⚠️
nf_core/__main__.py 93.33% 3 Missing ⚠️
nf_core/components/components_completion.py 87.50% 3 Missing ⚠️
... and 19 more

☔ View full report in Codecov by Sentry.
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mashehu
mashehu approved these changes Oct 15, 2025
View reviewed changes
@mirpedrol mirpedrol merged commit d0a40db into main Oct 15, 2025
209 checks passed
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