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Dev -> Master for 2.13 #2781
Dev -> Master for 2.13 #2781
Commits on Jan 30, 2024
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Commits on Feb 1, 2024
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Merge pull request #2721 from mirpedrol/bump-2.13dev
bump version to 2.13dev
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Commits on Feb 2, 2024
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Merge pull request #2724 from mashehu/update-ruff
update ruff for dev tools [skip changelog]
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Commits on Feb 3, 2024
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Commits on Feb 5, 2024
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need an extra empty line, otherwise html and markdown collide
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Merge pull request #2729 from nf-core/maxulysse-patch-4
Update README.md
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Commits on Feb 6, 2024
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Merge branch 'convert-create-lint-wf-action' of github.com:mashehu/to…
…ols into convert-create-lint-wf-action
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Merge pull request #2725 from mashehu/update-ruff-template
update ruff to 0.2.0 and add it to pre-commit step
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Merge pull request #2720 from nf-core/renovate/pin-dependencies
Pin dependencies
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Download CI Test: Set dev as the default branch and add customisation…
… option for manual dispatch.
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Merge pull request #2727 from MatthiasZepper/download_test_branch_fix
Pipeline template: Fix download test CI
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Merge pull request #2730 from nf-core/renovate/astral-sh-ruff-pre-com…
…mit-0.x Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1
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Commits on Feb 7, 2024
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Merge pull request #2706 from mashehu/fix-editorconfig
Avoid conflicts between editorconfig and prettier linting
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Merge pull request #2722 from mashehu/fix-files-unchanged-parital
fix ignoring changes in partial template files
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Merge branch 'force_checkout' of github.com:gregorysprenger/tools int…
…o force_checkout
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Commits on Feb 8, 2024
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Apply suggestions from code review
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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Merge pull request #2733 from mashehu/convert-create-lint-wf-action
make creat-lint-wf composable
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Merge pull request #2739 from nf-core/renovate/actions-setup-python-5.x
Update actions/setup-python action to v5
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Merge pull request #2738 from nf-core/renovate/actions-checkout-4.x
Update actions/checkout action to v4
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Merge pull request #2737 from nf-core/renovate/pin-dependencies
Pin dependencies
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Merge pull request #2742 from mirpedrol/jinja-fix
Template: fix jinja rendering of download_pipeline.yml
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Commits on Feb 9, 2024
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Merge pull request #2743 from nf-core/renovate/python-3.11-slim
Update python:3.11-slim Docker digest to 2a746e2
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Merge pull request #2740 from mashehu/fix-ci-error
only paths or paths-ignore is allowed for actions [skip changelog]
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Merge pull request #2744 from mashehu/make-filecmp-less-strict
linting: add looser comparison when linting pipeline logos
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Merge pull request #2734 from gregorysprenger/force_checkout
Handle dirty local module repos by force checkout of commits and branches if needed
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Merge pull request #2755 from nf-core/fix-gha-runners
Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors
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Merge pull request #2756 from nf-core/renovate/pin-dependencies
chore(deps): pin jlumbroso/free-disk-space action to 54081f1
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Merge branch 'switch-to-md-api-docs' of github.com:mashehu/tools into…
… switch-to-md-api-docs
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Commits on Feb 16, 2024
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Merge pull request #2757 from RaqManzano/RaqManzano-patch-1
Template: Fix GitHub Actions CI and Linting badges links
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Merge pull request #2736 from nf-core/rm_lib
Remove lib directory and replace it with granular utils_* subworkflows
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Merge pull request #2761 from mashehu/add-hashtags
template: add hashtags to release announcement on mastodon
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Merge pull request #2758 from mashehu/switch-to-md-api-docs
Switch to markdown based API and linting error docs
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Commits on Feb 17, 2024
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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Merge pull request #2767 from mashehu/nf-test-profiles
Modules: Add `--profile` parameter to nf-test command
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Merge pull request #2772 from mashehu/fix-api-build-request
fix github action syntax, remove now unneeded makefile [skip changelog]
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Merge pull request #2762 from mashehu/fix-lint-multiple-module-import
Linting: Handle multiple aliases in module imports correctly during linting
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Merge pull request #2773 from mashehu/fix-api-build-request
fix api docs build request (next attempt) [skip changelog]
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Merge pull request #2763 from mashehu/keep-nf-config-files-on-compone…
…nt-update Modules: keep nextflow.config during `nf-core modules/subworkflows update`
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Merge pull request #2775 from mashehu/fix-build-script
fix generate api docs script, gsed-> sed [skip changelog]
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Merge pull request #2770 from mirpedrol/migrate-pytest-symlink
Modules: Handle symlinks when migrating pytest
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Merge pull request #2771 from mirpedrol/extra-module-file
Modules: patch: handle file not found when it is an added file to a module
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Merge branch 'update-template-modules' of github.com:mashehu/tools in…
…to update-template-modules
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Commits on Feb 20, 2024
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Merge pull request #2779 from mashehu/fix-ruff-setting
Update pyproject.toml for ruff 0.2.0 [skip changelog]
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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Merge pull request #2776 from mashehu/update-template-modules
update modules in template
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Merge pull request #2777 from mashehu/fix-missing-files-in-update
move also subdirectories during update [skip changelog]
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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Merge pull request #2778 from mashehu/bump-version-2_13
bump version to dev -> 2.13
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Merge pull request #2782 from mashehu/fix-rich-codex
Fix rich codex timeout [skip changelog]
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