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Dev -> Master for 2.13.1#2811

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mashehu merged 59 commits intomasternf-core/tools:masterfrom devnf-core/tools:devCopy head branch name to clipboardFeb 29, 2024

+2,404-2,036

Commits

Commits on Feb 20, 2024

• bump version to 3.0dev

  mirpedrol

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Commits on Feb 21, 2024

• update badges

  maxulysse

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• add nf-test badge

  maxulysse

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• fix typo

  maxulysse

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• unit-tests

  maxulysse

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• use jinja

  maxulysse

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• Merge pull request #2783 from mirpedrol/bump-3.0dev

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  mashehu

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• Merge branch 'dev' into template_update

  mashehu

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• Merge pull request #2785 from maxulysse/template_update

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Commits on Feb 23, 2024

• chore(deps): update seqeralabs/action-tower-launch digest to aa88624

  renovate[bot]

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• [automated] Update CHANGELOG.md

  

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Commits on Feb 25, 2024

• chore(deps): update codecov/codecov-action digest to 0cfda1d

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• [automated] Update CHANGELOG.md

  

  nf-core-bot

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• fix(devcontainer): remove deprecated linters

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  kenibrewer

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Commits on Feb 27, 2024

• copy changes over to template, update extensions in gitpod.yml

  mashehu

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• update changelog

  mashehu

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• Merge pull request #2795 from kenibrewer/fix/remove-deprecated-linters

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• Write a new helper function: gather_registries() to read the config.

  MatthiasZepper

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• nf-core download: Write function to symlink containers to different libraries (registries).

  MatthiasZepper

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• Refactor: Always trim registry from output name. Naming collisions are presumably unlikely, names including the registry are now consistently always symlinks.

  MatthiasZepper

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• Modify the pytest.yml action such that Singularity is used for the nf-core download tests.

  MatthiasZepper

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• Extend ContainerError to match ghcr.io error message.

  MatthiasZepper

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• Add test_gather_registries() to test_download.py

  MatthiasZepper

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• Finally a comprehensive test for symlink_singularity_images()

  MatthiasZepper

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• Changelog.

  MatthiasZepper

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• Apply @Aratz 's suggestions from code review

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  Aratz

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• Improved the documentation of the singularity_image_filenames() function.

  MatthiasZepper

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• Added a test for the so far untested singularity_image_filenames() function.

  MatthiasZepper

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• Fixed a typo in the template

  nvnieuwk

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• Merge branch 'dev' into nvnieuwk-patch-1

  nvnieuwk

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• Merge pull request #2798 from nf-core/nvnieuwk-patch-1

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• chore(deps): update gitpod/workspace-base docker digest to c15ee2f

  renovate[bot]

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• [automated] Update CHANGELOG.md

  

  nf-core-bot

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• Added a few type hints and opened Pandoras box.

  MatthiasZepper

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Commits on Feb 28, 2024

• Unpin pinned dependecies for tower actions

  FriederikeHanssen

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• [automated] Update CHANGELOG.md

  nf-core-bot

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• add nf-test test instructions to contributing and PR template

  sateeshperi

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Commits on Feb 29, 2024

• update changelog

  sateeshperi

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• Merge pull request #2807 from nf-core/feat/add-nf-test-run-debug-instructions

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  sateeshperi

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• bump version to 2.13.1 [skip changelog]

  mashehu

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• fix changelog

  mashehu

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• Merge pull request #2768 from MatthiasZepper/download_image_naming_issue

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• Merge branch 'dev' into bump-version-2_13_1

  mashehu

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• Merge pull request #2809 from mashehu/bump-version-2_13_1

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• Template: Fix topic extraction step for hashtags in toots

  mashehu

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• Template: Update modules and subworkflows

  mashehu

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• fix md syntax in contributing

  mashehu

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• only run automated changelog on PRs to dev

  mashehu

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• Merge pull request #2812 from mashehu/update-template-modules

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• Merge branch 'dev' into fix-toot-hashtags

  mashehu

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• unpin setup-nextflow

  mashehu

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• chore(deps): update actions/download-artifact digest to 87c5514

  renovate[bot]

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• chore(deps): update codecov/codecov-action digest to 54bcd87

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• Merge pull request #2806 from FriederikeHanssen/unpin

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• Apply suggestions from code review

  mashehu

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• Merge pull request #2813 from mashehu/fix-syntax-in-contributing

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• Generate new screengrabs with rich-codex

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• Merge branch 'dev' into fix-toot-hashtags

  mashehu

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• Merge pull request #2810 from mashehu/fix-toot-hashtags

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