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Dev -> Master for v3.0.0 #3197

Merged
merged 940 commits into from
Oct 8, 2024
Merged

Dev -> Master for v3.0.0 #3197

merged 940 commits into from
Oct 8, 2024

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mirpedrol
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mirpedrol and others added 30 commits August 26, 2024 11:52
@mirpedrol
add option to exclude fastqc from pipeline template
f2b282c
@nf-core-bot @mirpedrol
[automated] Update CHANGELOG.md
e4f685d
@mirpedrol
don't fail when no nf-core modules installed
0e4a7d1
@mirpedrol
fix versions yaml file name
92618ad
@mirpedrol
udpate bpipe and fix pytests
d437582
@mirpedrol @mashehu
Apply suggestions from code review
9551cdc 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@mirpedrol
update textual snapshots
9d29e93
@mirpedrol
Merge pull request #3129 from mirpedrol/template-customisation-fastqc
2eb5458 
Template: add option to exclude fastqc from pipeline template
@nf-core-bot @mirpedrol
[automated] Update CHANGELOG.md
52da9e3
@mirpedrol @mashehu
Apply suggestions from code review
a8cb940 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@mirpedrol
update textual snapshots
bcbed05
@mirpedrol
Merge pull request #3130 from mirpedrol/template-customisation-docume…
769c6fc 
…ntation

Template: add option to exclude documentation from pipeline template
@mirpedrol
add option to exclude test configs from pipeline template
d3d6345
@nf-core-bot @mirpedrol
[automated] Update CHANGELOG.md
b301c5c
@mirpedrol
update textual snapshots
4552219
@mirpedrol
filter generated matrix with yq
25030e3
@mirpedrol
Merge pull request #3133 from mirpedrol/template-customisation-testing
40a8bcb 
Template: add option to exclude test configs from pipeline template
@mirpedrol
add option to exclude tower.yml from pipeline template
498435b
@nf-core-bot @mirpedrol
[automated] Update CHANGELOG.md
0f96bb3
@nvnieuwk
update nf-schema subwf
b85ea4d
@nvnieuwk
Merge branch 'dev' into feat/linting-nf-schema
c538cfd
@mirpedrol
update textual snapshots
0dd8d6f
@nvnieuwk
fix some issues
0fb97db
@nvnieuwk
fix linting utils_nfschema_plugin
7dee447
@nvnieuwk
update utils subwfs
6d01b0f
@mirpedrol
Merge pull request #3134 from mirpedrol/template-customisation-tower
ee85104 
Template: add option to exclude tower.yml from pipeline template
@nvnieuwk
fix some linting issues
a7dcdd7
@nvnieuwk
Merge branch 'dev' into feat/linting-nf-schema
a77f5a1
@nvnieuwk
ruff
fcdf65b
@nvnieuwk
add linting doc for plugin_includes
56150dc
mashehu and others added 22 commits October 4, 2024 15:29
@mashehu
remove modules.json copy step in sync
fa1a01d
@mashehu
Merge pull request #3189 from mashehu/sync-modules
bb2b10d 
add API docs for .nf-core.yml
@MatthiasZepper
Improve the Github Action to test offline support better.
d6cd273
@MatthiasZepper
Add raw statements for template and update Singularity version in run…
ca5eaa5 
…ner.
@MatthiasZepper
Fix container image count calculation.
5c39ab8
@mirpedrol
Merge pull request #3190 from mirpedrol/template-newlines
f54e9eb 
fix template new lines
@renovate
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.6.9
8feb89b
@MatthiasZepper
Tidy Jinja template markup.
89961d6
@MatthiasZepper
The raw statements must not wrap other Jinja markup.
664fbfa
@MatthiasZepper
Merge pull request #3182 from MatthiasZepper/seqera_community_containers
b36c433 
Pipeline template: Modify download test action to capture the number of containers
@mashehu
Merge pull request #3150 from nf-core/renovate/astral-sh-ruff-pre-com…
78d7d8a 
…mit-0.x
@renovate
chore(deps): update python:3.12-slim docker digest to af4e85f
fc9c001
@mashehu
add pipeline name as an optional sync input
aa15820
@mashehu
Merge pull request #3194 from mashehu/add-input-to-sync-gha
6a2b0af 
add pipeline name as an optional sync input
@mashehu
fix for multiqc_config template for released pipelines
962f4b3
@mirpedrol
bump version to 3.0.0
baeb1df
@mashehu
update nf-core command in sync.yml
0865cd1
@mirpedrol
fix some more template newlines
f20f797
@mirpedrol
Merge pull request #3195 from mashehu/fix-whitespaces
938fd34 
fix whitespaces in rendered template
@mirpedrol
Merge branch 'dev' into renovate/textual-dev-1.x
baa88db
@mirpedrol
Merge pull request #3153 from nf-core/renovate/textual-dev-1.x
3d56fd1 
chore(deps): update dependency textual-dev to v1.6.1
@mirpedrol
Merge pull request #3196 from mirpedrol/bump-to-3-0-0
503843d 
bump version to 3.0.0
@codecov Codecov
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codecov bot commented Oct 7, 2024 •
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Codecov Report

Attention: Patch coverage is 71.94891% with 593 lines in your changes missing coverage. Please review.

Project coverage is 75.51%. Comparing base (1b7612c) to head (9489c1c).
Report is 943 commits behind head on master.

Files with missing lines Patch % Lines
nf_core/commands_modules.py 13.93% 105 Missing ⚠️
nf_core/commands_subworkflows.py 16.12% 78 Missing ⚠️
nf_core/commands_pipelines.py 55.78% 65 Missing ⚠️
nf_core/__main__.py 79.01% 64 Missing ⚠️
nf_core/modules/lint/__init__.py 57.69% 44 Missing ⚠️
nf_core/synced_repo.py 53.44% 27 Missing ⚠️
nf_core/modules/modules_json.py 78.78% 21 Missing ⚠️
nf_core/pipelines/schema.py 83.00% 17 Missing ⚠️
nf_core/modules/lint/meta_yml.py 83.13% 14 Missing ⚠️
nf_core/pipelines/sync.py 62.16% 14 Missing ⚠️
... and 31 more
Additional details and impacted files

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

mashehu
mashehu approved these changes Oct 8, 2024
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@mirpedrol mirpedrol merged commit 2141a1d into master Oct 8, 2024
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@mashehu mashehu mashehu approved these changes

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9 participants
@mirpedrol @mashehu @nf-core-bot @nvnieuwk @ewels @jfy133 @mahesh-panchal @maxulysse @MatthiasZepper