Code

dev -> main for 3.2.0 release#3428

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mirpedrol merged 47 commits intomainnf-core/tools:mainfrom devnf-core/tools:devCopy head branch name to clipboardJan 27, 2025

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Commits on Jan 20, 2025

• bump version to 3.2.0dev

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• Merge pull request #3409 from mirpedrol/bump-to-3.2.0

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Commits on Jan 21, 2025

• fix(1929): more type-gating

  awgymer

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• fix CHANGELOG.md

  

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• fix(1929): update subworkflow tests and add lint test markdown

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• Apply suggestions from code review

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• feat(1929): allow missing files when linting local modules

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• feat(1929): local linting option now *only* lints local modules. Add tests

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• feat(1929): don't ask for a module/subworkflow name to lint if linting local

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• feat(1929): add test for new pipeline lint check of local component dirs

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• feat(1929): run todo linting on local subworkflows

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• fix: Update to latest CHANGELOG

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• fix: Clean up CHANGELOG.md

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• Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.1.2

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• [automated] Update CHANGELOG.md

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• Fix 'process.shell' in nextflow.config

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• Merge branch 'dev' into fix-process-shell

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• [automated] Update CHANGELOG.md

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• Merge pull request #3416 from ewels/fix-process-shell

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• Remove automated release tweets

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• [automated] Update CHANGELOG.md

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• [automated] Update CHANGELOG.md

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• Merge pull request #3419 from ewels/remove-twitter-release-notifications

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Commits on Jan 22, 2025

• Merge branch 'dev' into 1929-local-modules-use-remote-format

  awgymer

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• fix: broken test. Need to assign component_dir to the parent dir if a local module is an nf file only

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• fix: Add new lint test to lint config pydantic model

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Commits on Jan 23, 2025

• Update python:3.12-slim Docker digest to 123be56 (#3421)

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• Update pre-commit hook astral-sh/ruff-pre-commit to v0.9.3

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• [automated] Fix code linting

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Commits on Jan 24, 2025

• Merge pull request #3256 from awgymer/1929-local-modules-use-remote-format

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Commits on Jan 27, 2025

• Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x

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• chore(deps): update dawidd6/action-download-artifact action to v8 (#3424)

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• fix mypy error

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• Merge pull request #3413 from nf-core/renovate/astral-sh-ruff-pre-commit-0.x

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• Merge branch 'dev' into renovate/editorconfig-checker-editorconfig-checker.python-3.x

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• Separate -o pipefail into separate list elements

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• [automated] Update CHANGELOG.md

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• Merge pull request #3414 from nf-core/renovate/editorconfig-checker-editorconfig-checker.python-3.x

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• Merge pull request #3425 from ewels/o-pipefail-newline

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• update template components

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• [automated] Update CHANGELOG.md

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• Merge pull request #3426 from mirpedrol/update-template-modules

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• bump to v3.2.0

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• template line break fixes

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• Merge pull request #3427 from mirpedrol/bump-to-3.2.0

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• update changelog

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• Merge pull request #3429 from mirpedrol/changelog-updates

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