Code

dev -> main for 3.1.1#3369

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mirpedrol merged 89 commits intomainnf-core/tools:mainfrom devnf-core/tools:devCopy head branch name to clipboardDec 20, 2024

+142-71

Commits

Commits on Dec 10, 2024

• set default_branch to master for now

  mashehu

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• update changelog

  mashehu

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• Merge branch 'dev' into set-default-branch-to-master

  mashehu

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• Merge pull request #3335 from mashehu/set-default-branch-to-master

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  mashehu

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• set git defaultBranch to master in sync action

  mashehu

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• update changelog

  mashehu

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• use nextflow.config to set defaultBranch

  mashehu

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• Merge pull request #3337 from mashehu/fix-init-branch-in-sync-action

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  mashehu

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• fix path for nextflow.config grep

  mashehu

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• Merge branch 'dev' of github.com:nf-core/tools into fix-sync-grep

  mashehu

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• change working dir when setting defaultBranch

  mashehu

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• fix Changelog

  mashehu

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• Be more verbose in approval check action

  mashehu

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• fix if clause

  mashehu

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• update changelog

  mashehu

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• add verbose mode to sync action

  mashehu

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• update changelog

  mashehu

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Commits on Dec 11, 2024

• Apply suggestions from code review

  mirpedrol

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• add input debug for workflow_dispatch sync action

  mirpedrol

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• Merge pull request #3339 from mashehu/add-verbose-mode-to-sync

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  mirpedrol

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• go back to original directory after configuring git defaultBranch

  mirpedrol

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• Merge pull request #3342 from mirpedrol/sync-default-branch

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  mirpedrol

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• add more debugging on sync GHA

  mirpedrol

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• Merge pull request #3345 from mirpedrol/sync-default-branch

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  mirpedrol

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• echo message to sync GHA

  mirpedrol

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• try exiting pipeline directory before saving defaultBranch

  mirpedrol

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• cleanup debugging echo

  mirpedrol

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• use same ref in checkout as triggered the workflow

  mashehu

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Commits on Dec 12, 2024

• Merge pull request #3347 from mashehu/specify-ref-in-sync-yml

  mashehu

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• don't set up loggin level to error

  mirpedrol

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• Merge pull request #3349 from mirpedrol/sync-debugging

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  mirpedrol

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• Revert "don't set up loggin level to error [no changelog]"

  mashehu

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• Merge pull request #3350 from nf-core/revert-3349-sync-debugging

  mashehu

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• Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml

  mirpedrol

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• Merge pull request #3338 from mashehu/more-verbose-awsfulltest-checks

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  mirpedrol

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• Replace Github environment usage in Download Action.

  MatthiasZepper

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• bump version to 3.1.1dev

  mashehu

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• only bump ro-crate if it already exists

  mashehu

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Commits on Dec 13, 2024

• Merge pull request #3353 from mashehu/bump-version-3_1_1dev

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  mirpedrol

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• Merge branch 'dev' into fix-ro-crate-in-bump-version

  mirpedrol

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• get max of 100 branch names

  mirpedrol

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• Merge pull request #3354 from mashehu/fix-ro-crate-in-bump-version

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  mirpedrol

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• fix including modules.config

  mirpedrol

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• [automated] Update CHANGELOG.md

  nf-core-bot

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• revert #3301 until we add linting from #2508

  mirpedrol

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• Apply suggestions from code review

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  MatthiasZepper

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  mashehu

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• Revert "don't set up loggin level to error [no changelog]"

  

  mashehu

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  MatthiasZepper

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• Be more verbose in approval check action

  

  mashehu

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  MatthiasZepper

  committed
  4958cf0

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• fix if clause

  

  mashehu

  authored and

  MatthiasZepper

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  4c32e47

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• update changelog

  

  mashehu

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  MatthiasZepper

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  e32293d

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• Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml

  

  mirpedrol

  authored and

  MatthiasZepper

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  f02d6bb

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• Merge pull request #3356 from mirpedrol/fix-include-modules-config

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  mirpedrol

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• Merge branch 'dev' into no_env_in_download_action

  MatthiasZepper

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• Add missing p

  jfy133

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• [automated] Update CHANGELOG.md

  nf-core-bot

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  4db108c

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• fix pre-commit linting failures

  mirpedrol

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• Merge pull request #3357 from nf-core/usage-typo-fix

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  sateeshperi

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• don't run prettier on ro-crate json file

  mirpedrol

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• run pre-commit from a git repo

  mirpedrol

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• [automated] Update CHANGELOG.md

  nf-core-bot

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• Remove endraw statement that 'nf-core pipelines' create does not like.

  MatthiasZepper

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• Merge pull request #3351 from MatthiasZepper/no_env_in_download_action

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Commits on Dec 16, 2024

• prettify template and printing .nf-core.yml

  mirpedrol

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• Merge branch 'dev' into fix-pre-commit-template

  mirpedrol

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• Remove Dumpler from ruamel yaml

  mirpedrol

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• don't create rocrate file when we skip the feature

  mirpedrol

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• fix more prettier modifications form the template

  mirpedrol

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• don't try running pre-commit if code-linters or github are not used in the template

  mirpedrol

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• more template prittier fixing

  mirpedrol

  committed
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• more prettier fixes

  mirpedrol

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• Merge pull request #3358 from mirpedrol/fix-pre-commit-template

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  mirpedrol

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Commits on Dec 17, 2024

• use manifest.contributors names if available, otherwise default to manifest.author

  mirpedrol

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• [automated] Update CHANGELOG.md

  nf-core-bot

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  ac7fd48

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• Merge pull request #3362 from mirpedrol/fix-3359-lint-repo

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  mirpedrol

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• properly parse the names form manifest.contributors

  mirpedrol

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• update changelog

  mirpedrol

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Commits on Dec 19, 2024

• LICENSE copyright to nf-core community, lint LICENSE file is a warning instead of a failure

  mirpedrol

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• [automated] Update CHANGELOG.md

  nf-core-bot

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• update changelog

  mirpedrol

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Commits on Dec 20, 2024

• Apply suggestions from code review

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  mirpedrol

  and

  SPPearce

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• use pipeline team in license for non-nf-core pipelines

  mirpedrol

  committed
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• Merge pull request #3364 from mirpedrol/fix-3361-rocrate-contributors

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• Merge pull request #3366 from mirpedrol/update-license-linting

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  mirpedrol

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• bump to 3.1.1 for release

  mirpedrol

  committed
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• small modification of license, adding pipeline team

  mirpedrol

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• Merge pull request #3368 from mirpedrol/license-modification

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• Merge pull request #3367 from mirpedrol/bump-3.1.1

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  mirpedrol

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• Merge branch 'main' into dev

  mirpedrol

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• don't lint ro-crate file

  mirpedrol

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