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Dev -> Master for 2.13 #2781

Merged
merged 241 commits into from
Feb 20, 2024
Merged

Dev -> Master for 2.13 #2781

merged 241 commits into from
Feb 20, 2024

Commits on Jan 30, 2024

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  4. remove ignored option

    mashehu committed Jan 30, 2024
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Commits on Feb 1, 2024

  1. bump to 2.13dev

    mirpedrol committed Feb 1, 2024
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  2. Merge pull request #2721 from mirpedrol/bump-2.13dev

    bump version to 2.13dev
    mirpedrol authored Feb 1, 2024
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  5. fix changelog

    mashehu committed Feb 1, 2024
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  6. fix one more path

    mashehu committed Feb 1, 2024
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Commits on Feb 2, 2024

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  4. Merge pull request #2724 from mashehu/update-ruff

    update ruff for dev tools [skip changelog]
    mashehu authored Feb 2, 2024
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  5. fix docstring

    mashehu committed Feb 2, 2024
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Commits on Feb 3, 2024

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Commits on Feb 5, 2024

  1. Update README.md

    need an extra empty line, otherwise html and markdown collide
    maxulysse authored Feb 5, 2024
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  3. fix changelog

    mashehu committed Feb 5, 2024
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  4. Merge pull request #2729 from nf-core/maxulysse-patch-4

    Update README.md
    maxulysse authored Feb 5, 2024
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Commits on Feb 6, 2024

  1. Pin dependencies

    renovate[bot] authored Feb 6, 2024
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  7. move to correct folder

    mashehu committed Feb 6, 2024
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  9. fix composite action syntax

    mashehu committed Feb 6, 2024
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  10. Merge branch 'convert-create-lint-wf-action' of github.com:mashehu/to…

    …ols into convert-create-lint-wf-action
    mashehu committed Feb 6, 2024
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  11. fix action syntax

    mashehu committed Feb 6, 2024
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  12. clean up actions

    mashehu committed Feb 6, 2024
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  13. Merge pull request #2725 from mashehu/update-ruff-template

    update ruff to 0.2.0 and add it to pre-commit step
    mashehu authored Feb 6, 2024
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  15. Merge pull request #2720 from nf-core/renovate/pin-dependencies

    Pin dependencies
    mashehu authored Feb 6, 2024
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  16. Download CI Test: Set dev as the default branch and add customisation…

    … option for manual dispatch.
    MatthiasZepper committed Feb 6, 2024
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  17. Update Changelog.

    MatthiasZepper committed Feb 6, 2024
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  18. fix trailing whitespace

    mashehu committed Feb 6, 2024
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  19. Merge pull request #2727 from MatthiasZepper/download_test_branch_fix

    Pipeline template: Fix download test CI
    mashehu authored Feb 6, 2024
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  20. 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
    mashehu authored Feb 6, 2024
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Commits on Feb 7, 2024

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  2. Merge pull request #2706 from mashehu/fix-editorconfig

    Avoid conflicts between editorconfig and prettier linting
    mashehu authored Feb 7, 2024
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  4. Merge pull request #2722 from mashehu/fix-files-unchanged-parital

    fix ignoring changes in partial template files
    mashehu authored Feb 7, 2024
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  9. fix tests

    mashehu committed Feb 7, 2024
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Commits on Feb 8, 2024

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  9. fix syntax

    mashehu committed Feb 8, 2024
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  14. one more

    mashehu committed Feb 8, 2024
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  16. debug workflow

    mashehu committed Feb 8, 2024
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  17. add shell

    mashehu committed Feb 8, 2024
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  18. remove clean up action

    mashehu committed Feb 8, 2024
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  19. Apply suggestions from code review

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    mashehu and mirpedrol authored Feb 8, 2024
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  20. Merge pull request #2733 from mashehu/convert-create-lint-wf-action

    make creat-lint-wf composable
    mashehu authored Feb 8, 2024
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  25. Merge pull request #2739 from nf-core/renovate/actions-setup-python-5.x

    Update actions/setup-python action to v5
    mashehu authored Feb 8, 2024
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  28. Merge pull request #2738 from nf-core/renovate/actions-checkout-4.x

    Update actions/checkout action to v4
    mashehu authored Feb 8, 2024
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  29. Pin dependencies

    renovate[bot] authored Feb 8, 2024
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  30. Merge pull request #2737 from nf-core/renovate/pin-dependencies

    Pin dependencies
    mashehu authored Feb 8, 2024
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  31. Merge pull request #2742 from mirpedrol/jinja-fix

    Template: fix jinja rendering of download_pipeline.yml
    MatthiasZepper authored Feb 8, 2024
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Commits on Feb 9, 2024

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  3. Merge pull request #2743 from nf-core/renovate/python-3.11-slim

    Update python:3.11-slim Docker digest to 2a746e2
    mashehu authored Feb 9, 2024
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  6. Merge pull request #2740 from mashehu/fix-ci-error

    only paths or paths-ignore is allowed for actions [skip changelog]
    mashehu authored Feb 9, 2024
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Commits on Feb 10, 2024

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Commits on Feb 12, 2024

  1. Merge pull request #2744 from mashehu/make-filecmp-less-strict

    linting: add looser comparison when linting pipeline logos
    mashehu authored Feb 12, 2024
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Commits on Feb 13, 2024

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  2. Merge pull request #2734 from gregorysprenger/force_checkout

    Handle dirty local module repos by force checkout of commits and branches if needed
    mashehu authored Feb 13, 2024
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  5. fix pytests

    mirpedrol committed Feb 13, 2024
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  9. [automated] Update CHANGELOG.md

    nf-core-bot authored and renovate[bot] committed Feb 13, 2024
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Commits on Feb 14, 2024

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  2. fix more pytests

    mirpedrol committed Feb 14, 2024
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  5. fix docstrings

    mashehu committed Feb 14, 2024
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  6. fix more docstrings

    mashehu committed Feb 14, 2024
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  9. fix more linting tests

    mirpedrol committed Feb 14, 2024
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Commits on Feb 15, 2024

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  4. optimize script

    mashehu committed Feb 15, 2024
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  9. Update README.md

    Fixed GitHub Actions CI and Linting badges links.
    RaqManzano authored Feb 15, 2024
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  11. Update CHANGELOG.md

    mashehu authored Feb 15, 2024
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  12. 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
    apeltzer authored Feb 15, 2024
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  16. Fix badge links

    ewels authored Feb 15, 2024
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  18. Merge pull request #2756 from nf-core/renovate/pin-dependencies

    chore(deps): pin jlumbroso/free-disk-space action to 54081f1
    mashehu authored Feb 15, 2024
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  19. fix changelog

    mashehu committed Feb 15, 2024
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  21. add missing remark script

    mashehu committed Feb 15, 2024
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  24. fix index pages

    mashehu committed Feb 15, 2024
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  25. update path for remark script

    mashehu committed Feb 15, 2024
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  27. remove typo

    mashehu committed Feb 15, 2024
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  30. add debugging

    mashehu committed Feb 15, 2024
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  32. remove debugging

    mashehu committed Feb 15, 2024
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  34. tidy up remark code

    mashehu committed Feb 15, 2024
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  35. fix one more index page

    mashehu committed Feb 15, 2024
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  36. use different remark logic

    mashehu committed Feb 15, 2024
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  37. Merge branch 'switch-to-md-api-docs' of github.com:mashehu/tools into…

    … switch-to-md-api-docs
    mashehu committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. fix api index page

    mashehu committed Feb 16, 2024
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  2. Merge pull request #2757 from RaqManzano/RaqManzano-patch-1

    Template: Fix GitHub Actions CI and Linting badges links
    mashehu authored Feb 16, 2024
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  3. Merge pull request #2736 from nf-core/rm_lib

    Remove lib directory and replace it with granular utils_* subworkflows
    mirpedrol authored Feb 16, 2024
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  7. Apply suggestions from code review

    Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
    mashehu and jfy133 authored Feb 16, 2024
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  8. add profile parameter to nf-test command

    fixes #2753
    mashehu committed Feb 16, 2024
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  9. handle multiple module imports in linting

    closes #2726
    mashehu committed Feb 16, 2024
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  11. fix changelog

    mashehu committed Feb 16, 2024
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  12. Merge pull request #2761 from mashehu/add-hashtags

    template: add hashtags to release announcement on mastodon
    mashehu authored Feb 16, 2024
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  13. fix tests

    mashehu committed Feb 16, 2024
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  14. add prompt for extra files

    mashehu committed Feb 16, 2024
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  15. Merge pull request #2758 from mashehu/switch-to-md-api-docs

    Switch to markdown based API and linting error docs
    mashehu authored Feb 16, 2024
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  20. fix tests

    mashehu committed Feb 16, 2024
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  22. fix all occurences

    mashehu committed Feb 16, 2024
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  23. remove options

    mashehu committed Feb 16, 2024
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  24. simplify logic and add tests

    mashehu committed Feb 16, 2024
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Commits on Feb 17, 2024

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Commits on Feb 18, 2024

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Commits on Feb 19, 2024

  1. add test for symlink deletion

    mashehu committed Feb 19, 2024
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  2. Update CHANGELOG.md

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    mashehu and mirpedrol authored Feb 19, 2024
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  4. fix action name

    mashehu committed Feb 19, 2024
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  6. Merge pull request #2767 from mashehu/nf-test-profiles

    Modules: Add `--profile` parameter to nf-test command
    mashehu authored Feb 19, 2024
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  7. Merge pull request #2772 from mashehu/fix-api-build-request

    fix github action syntax, remove now unneeded makefile [skip changelog]
    mashehu authored Feb 19, 2024
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  8. Merge pull request #2762 from mashehu/fix-lint-multiple-module-import

    Linting: Handle multiple aliases in module imports correctly during linting
    mashehu authored Feb 19, 2024
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  9. add missing comma

    mashehu committed Feb 19, 2024
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  10. Merge pull request #2773 from mashehu/fix-api-build-request

    fix api docs build request (next attempt) [skip changelog]
    mashehu authored Feb 19, 2024
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  12. fix test name

    mashehu committed Feb 19, 2024
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  14. Merge pull request #2763 from mashehu/keep-nf-config-files-on-compone…

    …nt-update
    
    Modules: keep nextflow.config during `nf-core modules/subworkflows update`
    mashehu authored Feb 19, 2024
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  17. Merge pull request #2775 from mashehu/fix-build-script

    fix generate api docs script, gsed-> sed  [skip changelog]
    mashehu authored Feb 19, 2024
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  18. Merge pull request #2770 from mirpedrol/migrate-pytest-symlink

    Modules: Handle symlinks when migrating pytest
    mirpedrol authored Feb 19, 2024
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  20. Merge pull request #2771 from mirpedrol/extra-module-file

    Modules: patch: handle file not found when it is an added file to a module
    mirpedrol authored Feb 19, 2024
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  21. update modules in template

    mashehu committed Feb 19, 2024
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  24. bring back lost files

    mashehu committed Feb 19, 2024
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  25. Merge branch 'update-template-modules' of github.com:mashehu/tools in…

    …to update-template-modules
    mashehu committed Feb 19, 2024
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  26. fix changelog

    mashehu committed Feb 19, 2024
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  27. bump version to dev -> 2.13

    mashehu committed Feb 19, 2024
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Commits on Feb 20, 2024

  1. add code review suggestions

    mashehu committed Feb 20, 2024
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  3. format pyproject.toml file

    mashehu committed Feb 20, 2024
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  5. Merge pull request #2779 from mashehu/fix-ruff-setting

    Update pyproject.toml for ruff 0.2.0 [skip changelog]
    mashehu authored Feb 20, 2024
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  7. Update CHANGELOG.md

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    mashehu and mirpedrol authored Feb 20, 2024
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  8. Merge pull request #2776 from mashehu/update-template-modules

    update modules in template
    mashehu authored Feb 20, 2024
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  9. Merge pull request #2777 from mashehu/fix-missing-files-in-update

    move also subdirectories during update [skip changelog]
    mashehu authored Feb 20, 2024
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  10. Update CHANGELOG.md

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    mashehu and mirpedrol authored Feb 20, 2024
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  13. [automated] Update CHANGELOG.md

    nf-core-bot authored and renovate[bot] committed Feb 20, 2024
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  14. Merge pull request #2778 from mashehu/bump-version-2_13

    bump version to dev -> 2.13
    mashehu authored Feb 20, 2024
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  17. Merge pull request #2782 from mashehu/fix-rich-codex

    Fix rich codex timeout [skip changelog]
    mashehu authored Feb 20, 2024
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  19. update changelog

    mirpedrol authored Feb 20, 2024
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