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Dev -> main for 3.0.2 #3219

Merged
merged 57 commits into from
Oct 11, 2024
Merged

Dev -> main for 3.0.2 #3219

merged 57 commits into from
Oct 11, 2024

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mashehu
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@mashehu mashehu commented Oct 11, 2024

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maxulysse and others added 30 commits October 4, 2024 13:42
@maxulysse
Update .gitignore
62ce0c9 
include null/ for people that forget outdir
@mashehu
bump version to 3.0.2dev
1c65b3b
@mashehu
Merge pull request #3211 from mashehu/bump-to-3_0_2dev
93a5bce 
bump version to 3.0.2dev
@mirpedrol
assign schema_default when a param is found in the schema but not in …
51bbd46 
…the config
@maxulysse
Parallelize pipeline GHA tests over docker/conda/singularity
972de9d
@mashehu
parse defaultIgnoreParams correctly
d4980ca
@nf-core-bot
[automated] Fix code linting
8ab88cb
@mashehu
Merge pull request #3213 from mirpedrol/fix-params-validation
16dc3b9 
Linting: Fix bug when linting schema params
@maxulysse
fix GHA
ba6b661
@maxulysse
fix template strings
35d7e08
@maxulysse
add TODO
a1ff5e9
@maxulysse
Fix name
45012dd
@maxulysse
Merge branch 'dev' into maxulysse-patch-6
991fa5e
@maxulysse @mashehu
Apply suggestions from code review
27be623 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@maxulysse @mashehu
Update nf_core/pipeline-template/.github/workflows/ci.yml
eb2be9a 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@maxulysse
test -> test_name
1c8d74b
@maxulysse
Update nf_core/pipeline-template/.github/workflows/ci.yml
7556c0a
@maxulysse
more comments
b51770c
@maxulysse
Update nf_core/pipeline-template/.github/workflows/ci.yml
42f1de4
@mirpedrol
minimise raw and endraw blocks
ac3d577
@maxulysse
Update .gitignore
0c6f4b8
@maxulysse
Merge branch 'dev' into maxulysse-patch-5
e3e0a83
@maxulysse
Update CHANGELOG.md
71d348d
@maxulysse
Update CHANGELOG.md
853060b
@maxulysse
Merge pull request #3191 from nf-core/maxulysse-patch-5
3b8cd7f 
TEMPLATE: Add null/ to .gitignore
@maxulysse
Merge branch 'dev' into maxulysse-patch-6
dfe65d4
@maxulysse @mashehu
Update nf_core/pipeline-template/.github/workflows/ci.yml
3bd7105 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@maxulysse
Merge pull request #3214 from nf-core/maxulysse-patch-6
88dc61c 
TEMPLATE: Parallelize pipeline GHA tests over docker/conda/singularity
@mashehu @mirpedrol
fix version of yaml action and change trigger event
dfec2cc
@mashehu @mirpedrol
checkout out the PR code, change styling of message
06f8b4d
mirpedrol and others added 24 commits October 11, 2024 07:07
@mirpedrol
update changelog
1b429cb
@mirpedrol
Merge pull request #3212 from mashehu/fix-template-version-comment-ac…
5d368d7 
…tion

TEMPLATE: Fix version comment action
@mashehu
remove last mentions of old cli commands
3a0ff6d
@mirpedrol
bump version to 3.0.2
9a395ad
@ewels
Merge branch 'dev' into fix-pipeline-commands-in-docstrings
f8b2335
@mashehu
fix changelog
1071a30
@mashehu
Merge branch 'fix-pipeline-commands-in-docstrings' of github.com:mash…
7f9f4d7 
…ehu/tools into fix-pipeline-commands-in-docstrings
@mashehu
add missing section into changelog
945c921
@nf-core-bot
[automated] Update CHANGELOG.md
d9776bf
@mashehu @maxulysse
Update CHANGELOG.md
07a0c62 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@mashehu
Merge pull request #3215 from mashehu/fix-pipeline-commands-in-docstr…
310046d 
…ings

Use updated pipeline commands in docstrings
@mirpedrol @mashehu
Update CHANGELOG.md
807a11e 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mirpedrol
Merge branch 'dev' into bump-to-3.0.2
7266eb2
@mashehu
disable automatic sync on release, fix handling empty pipeline name f…
dd2d130 
…ield
@mashehu
update changelog
24fe05d
@mirpedrol
update textual snapshots
eb7eaf9
@mashehu
Merge pull request #3217 from mashehu/fix-sync-action
a5a86c0 
disable automatic sync on release, fix handling empty pipeline input
@mirpedrol
Merge pull request #3216 from mirpedrol/bump-to-3.0.2
9bdae65 
bump version to 3.0.2 [skip changelog]
@mirpedrol
fix pre-commit lining failing on pipelines template
f59c5f3
@mirpedrol
use multi-line string for local swf
12084b4
@mirpedrol
update changelog
f2339a3
@mirpedrol
update template components
cc713d8
@mirpedrol
fix small typo
658f77b
@mirpedrol
Merge pull request #3218 from mirpedrol/fix-editorconfig
9cdc2da 
Template: fix pre-commit lining failing on pipelines template
mirpedrol
mirpedrol approved these changes Oct 11, 2024
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LGTM 🚀

@codecov Codecov
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codecov bot commented Oct 11, 2024

Codecov Report

Attention: Patch coverage is 80.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 75.51%. Comparing base (3a706f0) to head (9cdc2da).
Report is 3 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/pipelines/lint/nextflow_config.py 0.00% 1 Missing ⚠️
Additional details and impacted files

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

apeltzer
apeltzer approved these changes Oct 11, 2024
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Thanks for working on this so quickly. Looks good to me and I've tried using some of the template changes in our PR and it worked nicely there.

@mashehu mashehu merged commit ddb58c2 into main Oct 11, 2024
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@apeltzer apeltzer apeltzer approved these changes

@mirpedrol mirpedrol mirpedrol approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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6 participants
@mashehu @apeltzer @mirpedrol @maxulysse @nf-core-bot @ewels