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Continuation of #3083#3456

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mirpedrol wants to merge 81 commits intodevnf-core/tools:devfrom pr_3083nf-core/tools:pr_3083Copy head branch name to clipboard

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Commits on Jun 21, 2024

• tests: Add test case for cross-organization subwf

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Commits on Jun 28, 2024

• tests: Check module on module list instead

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Commits on Jul 1, 2024

• chore: Dummy commit to test action

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• Revert "chore: Dummy commit to test action"

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Commits on Jul 2, 2024

• tests: Change installed subworkflow

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Commits on Jul 8, 2024

• Merge pull request #6 from sanger-tol/cross-org-test

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• feat: Read from meta.yml in get_components_to_install

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Commits on Jul 15, 2024

• refact: Change module return type to always be dict

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• fix: Add correct return type

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• fix: Use any for values

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Commits on Jul 28, 2024

• test: Fix module key in across orgs

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• refact: Reset modules repo when git_remote not defined

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• refact: Copy parent attribute

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• refact: Keep old strategy as fallback

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• refact: Check component not in subwf list

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• refact: Change return type to optional

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• refact: Change way of handling dicts in modulesjson

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• refact: Handle dicts in meta_yml lint

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• fix: Pass branch in install too

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Commits on Aug 5, 2024

• fix: Check if module in meta.yml is imported

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• Merge pull request #9 from sanger-tol/fix/duplicated-downloads

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• Merge branch 'dev' into fix/1927

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Commits on Aug 10, 2024

• Merge branch 'dev' into review-round-1

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• refact: Define org path based on git remote

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• feat: Allow defining branches in meta.yml

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• fix: Add empty branch in other dicts

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Commits on Aug 12, 2024

• refact: Rework logic to use subwfs as well

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• refact: Support subwf dict in recreate deps

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• fix: Change modules to subwfs

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• fix: Use name value in recreate deps

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• Revert "fix: Use name value in recreate deps"

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• fix: Use subworkflow name in recreate deps

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• fix: Use sw_name in appends too

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• Merge branch 'dev' into fix/1927

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• Merge branch 'fix/1927' into review-round-1

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• Merge branch 'feat/use-subwf' into review-round-1

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• fix: Only add module if it's in main.nf too

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Commits on Aug 13, 2024

• fix: Handle incomplete meta.yml

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• refact: Remove isinstance check in lint/meta.yml

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• style: Format meta_yml.py

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• refact: Remove isinstance check in components/install.py

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• Revert "refact: Remove isinstance check in components/install.py"

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• refact: Remove isinstance check in recreate_deps

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• Merge pull request #10 from sanger-tol/review-round-1

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• Merge branch 'dev' into merge-dev

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• Merge pull request #11 from sanger-tol/merge-dev

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Commits on Aug 15, 2024

• refact: Change function structure to use dicts not lists

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• fix: Change access key in inner dicts

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Commits on Aug 16, 2024

• refact: Use component_name every time

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• refact: Don't default to master

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Commits on Aug 20, 2024

• refact: Move instance check up

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• Refactoring of component_utils.py

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• Revert "Refactoring of component_utils.py"

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Commits on Aug 21, 2024

• refact: Use get in components/install.py

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• refact: Avoid redefining keys when possible

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• refact: Use get in modules_json

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• refact: Use dictionary input in check_up_to_date

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• Use the power of get to skip if tests

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• Merge pull request #13 from sanger-tol/refact/change_structure_leverage_get

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Commits on Aug 22, 2024

• refact: Raise error if org_path not found

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• style: Run ruff format

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• refact: Change UserWarning message

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• style: Run ruff format

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• Merge pull request #12 from sanger-tol/refact/change_structure

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Commits on Aug 23, 2024

• Merge remote-tracking branch 'upstream/dev' into merge-dev2

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Commits on Sep 2, 2024

• Merge remote-tracking branch 'upstream/dev' into fix/1927

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Commits on Sep 6, 2024

• refact: Use walrus operator in meta.yml check

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• refact: Use a union type for component arg

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• Merge remote-tracking branch 'upstream/dev' into second-review

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Commits on Sep 9, 2024

• Merge pull request #14 from sanger-tol/second-review

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Commits on Sep 13, 2024

• docs: Add comment for clarification about the feature

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Commits on Dec 4, 2024

• refact: Add suggestions from the third round of reviews (#15)

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• Merge dev third rev (#20)

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• Merge branch 'dev' into fix/1927

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Commits on Dec 16, 2024

• refact: Use same org_path as modulesrepo first (#22)

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• Squashed commit of the following:

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• Merge branch 'dev' into fix/1927

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• test: Use correct org name in remove (#23)

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Commits on Feb 19, 2025

• Merge branch 'dev' of https://github.com/nf-core/tools into fix/1927

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• [automated] Update CHANGELOG.md

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• remove cross-components when removing a subworkflow

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