Dev -> main for 3.0.2 #3219

mashehu · 2024-10-11T10:46:46Z

No description provided.

include null/ for people that forget outdir

bump version to 3.0.2dev

…the config

Linting: Fix bug when linting schema params

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

TEMPLATE: Add null/ to .gitignore

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

TEMPLATE: Parallelize pipeline GHA tests over docker/conda/singularity

…tion TEMPLATE: Fix version comment action

…ehu/tools into fix-pipeline-commands-in-docstrings

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

…ings Use updated pipeline commands in docstrings

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

…ield

disable automatic sync on release, fix handling empty pipeline input

bump version to 3.0.2 [skip changelog]

Template: fix pre-commit lining failing on pipelines template

mirpedrol

LGTM 🚀

codecov · 2024-10-11T11:02:52Z

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

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apeltzer

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.

maxulysse and others added 30 commits October 4, 2024 13:42

Update .gitignore

62ce0c9

include null/ for people that forget outdir

bump version to 3.0.2dev

1c65b3b

Merge pull request #3211 from mashehu/bump-to-3_0_2dev

93a5bce

bump version to 3.0.2dev

assign schema_default when a param is found in the schema but not in …

51bbd46

…the config

Parallelize pipeline GHA tests over docker/conda/singularity

972de9d

parse defaultIgnoreParams correctly

d4980ca

[automated] Fix code linting

8ab88cb

Merge pull request #3213 from mirpedrol/fix-params-validation

16dc3b9

Linting: Fix bug when linting schema params

fix GHA

ba6b661

fix template strings

35d7e08

add TODO

a1ff5e9

Fix name

45012dd

Merge branch 'dev' into maxulysse-patch-6

991fa5e

Apply suggestions from code review

27be623

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update nf_core/pipeline-template/.github/workflows/ci.yml

eb2be9a

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

test -> test_name

1c8d74b

Update nf_core/pipeline-template/.github/workflows/ci.yml

7556c0a

more comments

b51770c

Update nf_core/pipeline-template/.github/workflows/ci.yml

42f1de4

minimise raw and endraw blocks

ac3d577

Update .gitignore

0c6f4b8

Merge branch 'dev' into maxulysse-patch-5

e3e0a83

Update CHANGELOG.md

71d348d

Update CHANGELOG.md

853060b

Merge pull request #3191 from nf-core/maxulysse-patch-5

3b8cd7f

TEMPLATE: Add null/ to .gitignore

Merge branch 'dev' into maxulysse-patch-6

dfe65d4

Update nf_core/pipeline-template/.github/workflows/ci.yml

3bd7105

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge pull request #3214 from nf-core/maxulysse-patch-6

88dc61c

TEMPLATE: Parallelize pipeline GHA tests over docker/conda/singularity

fix version of yaml action and change trigger event

dfec2cc

checkout out the PR code, change styling of message

06f8b4d

mirpedrol and others added 24 commits October 11, 2024 07:07

update changelog

1b429cb

Merge pull request #3212 from mashehu/fix-template-version-comment-ac…

5d368d7

…tion TEMPLATE: Fix version comment action

remove last mentions of old cli commands

3a0ff6d

bump version to 3.0.2

9a395ad

Merge branch 'dev' into fix-pipeline-commands-in-docstrings

f8b2335

fix changelog

1071a30

Merge branch 'fix-pipeline-commands-in-docstrings' of github.com:mash…

7f9f4d7

…ehu/tools into fix-pipeline-commands-in-docstrings

add missing section into changelog

945c921

[automated] Update CHANGELOG.md

d9776bf

Update CHANGELOG.md

07a0c62

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Merge pull request #3215 from mashehu/fix-pipeline-commands-in-docstr…

310046d

…ings Use updated pipeline commands in docstrings

Update CHANGELOG.md

807a11e

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge branch 'dev' into bump-to-3.0.2

7266eb2

disable automatic sync on release, fix handling empty pipeline name f…

dd2d130

…ield

update changelog

24fe05d

update textual snapshots

eb7eaf9

Merge pull request #3217 from mashehu/fix-sync-action

a5a86c0

disable automatic sync on release, fix handling empty pipeline input

Merge pull request #3216 from mirpedrol/bump-to-3.0.2

9bdae65

bump version to 3.0.2 [skip changelog]

fix pre-commit lining failing on pipelines template

f59c5f3

use multi-line string for local swf

12084b4

update changelog

f2339a3

update template components

cc713d8

fix small typo

658f77b

Merge pull request #3218 from mirpedrol/fix-editorconfig

9cdc2da

Template: fix pre-commit lining failing on pipelines template

mashehu requested review from mirpedrol and maxulysse October 11, 2024 10:46

mirpedrol approved these changes Oct 11, 2024

View reviewed changes

apeltzer approved these changes Oct 11, 2024

View reviewed changes

mashehu merged commit ddb58c2 into main Oct 11, 2024
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Dev -> main for 3.0.2 #3219

Dev -> main for 3.0.2 #3219

mashehu commented Oct 11, 2024

mirpedrol left a comment

codecov bot commented Oct 11, 2024

apeltzer left a comment

Dev -> main for 3.0.2 #3219

Dev -> main for 3.0.2 #3219

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