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Migrate component create to nf test #2490

Merged
merged 119 commits into from
Nov 21, 2023
Merged

Migrate component create to nf test #2490

merged 119 commits into from
Nov 21, 2023

Commits on Oct 24, 2023

  1. generalize nextflow_cmd to run_cmd to use the same structure for nf-test

    @mashehu
    mashehu committed Oct 24, 2023
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  2. initial changes for nf-test

    @mashehu
    mashehu committed Oct 24, 2023
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  3. move tags.yml to correct position

    @mashehu
    mashehu committed Oct 24, 2023
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  4. Update nf_core/utils.py 

    Co-authored-by: Júlia Mir Pedrol <[email protected]>
    @mashehu @mirpedrol
    mashehu and mirpedrol authored Oct 24, 2023
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  5. convert all cmds

    @mashehu
    mashehu committed Oct 24, 2023
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  6. first running version

    @mashehu
    mashehu committed Oct 24, 2023
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  7. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Oct 24, 2023
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  8. replace params

    @mashehu
    mashehu committed Oct 24, 2023
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  9. fix typing errors

    @mashehu
    mashehu committed Oct 24, 2023
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Commits on Oct 25, 2023

  1. add TODO comments to main.nf.test and fix tags.yml template rendering

    @mirpedrol
    mirpedrol committed Oct 25, 2023
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  2. add todo comment for chained modules

    @mirpedrol
    mirpedrol committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. add real example to main.nf.test

    @mirpedrol
    mirpedrol committed Oct 26, 2023
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  2. add tags.yml to prettierignore

    @mirpedrol
    mirpedrol committed Oct 26, 2023
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  3. add main.nf.test to template instead of using nf-test

    @mirpedrol
    mirpedrol committed Oct 26, 2023
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Commits on Oct 31, 2023

  1. generalize nextflow_cmd to run_cmd to use the same structure for nf-test

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  2. initial changes for nf-test

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  3. move tags.yml to correct position

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  4. convert all cmds

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  5. first running version

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  6. replace params

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  7. fix typing errors

    @mashehu @mirpedrol
    mashehu authored and mirpedrol committed Oct 31, 2023
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  8. add TODO comments to main.nf.test and fix tags.yml template rendering

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  9. add todo comment for chained modules

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  10. add real example to main.nf.test

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  11. add tags.yml to prettierignore

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  12. add main.nf.test to template instead of using nf-test

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  13. modules create tests check for main.nf.test

    @mirpedrol
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  14. remove outputDir from the modules template

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  15. add nf-test to subworkflows

    @mirpedrol
    mirpedrol committed Oct 31, 2023
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  16. subworkflows create tests check for main.nf.test

    @mirpedrol
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  17. Merge branch 'migrate-component-create-to-nf_test' of https://github.… 

    …com/mashehu/tools into migrate-component-create-to-nf_test
    @mirpedrol
    mirpedrol committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. fix tags for subtools, add version assertion to template

    @mashehu
    mashehu committed Nov 1, 2023
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  2. fix quotes in templates

    @mashehu
    mashehu committed Nov 1, 2023
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  3. add first version of the create-snapshot command

    @mashehu
    mashehu committed Nov 1, 2023
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  4. install all type specific dependencies in CI step

    @mashehu
    mashehu committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. add new command 🙃

    @mashehu
    mashehu committed Nov 2, 2023
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  2. remove tests for modules create_test_yml

    @mashehu
    mashehu committed Nov 2, 2023
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  3. remove more mentions of test_yml_builder

    @mashehu
    mashehu committed Nov 2, 2023
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  4. add types to create-snapshot and use component_type

    @mirpedrol
    mirpedrol committed Nov 2, 2023
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  5. add subworkflows create-snapshot

    @mirpedrol
    mirpedrol committed Nov 2, 2023
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Commits on Nov 6, 2023

  1. add linting for snapshot file

    @mashehu
    mashehu committed Nov 6, 2023
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  2. add correct tags to subworkflow template

    @mashehu
    mashehu committed Nov 6, 2023
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  3. fix smaller things according to mypy

    @mashehu
    mashehu committed Nov 6, 2023
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  4. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. add pytests for components snapshot generator

    @mirpedrol
    mirpedrol committed Nov 7, 2023
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  2. add more typing

    @mashehu
    mashehu committed Nov 7, 2023
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  3. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test

# Conflicts:
#	nf_core/components/snapshot_generator.py
    @mashehu
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  4. run create-snapshot tests from modules root directory

    @mirpedrol
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  5. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
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  6. fix checking if PROFILE exists

    @mirpedrol
    mirpedrol committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. add new environment.yml setup to template according to nf-core#2495 

    closes nf-core#2495
    @mashehu
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  2. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 8, 2023
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  3. use set_wd for tests

    @mirpedrol
    mirpedrol committed Nov 8, 2023
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  4. check md5sums and add snapshot test for a subworkflow

    @mirpedrol
    mirpedrol committed Nov 8, 2023
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  5. append error messages to self.errors

    @mashehu
    mashehu committed Nov 8, 2023
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  6. add --dir option to create-snapshot command

    @mirpedrol
    mirpedrol committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. add no test found error and test for this

    @mirpedrol
    mirpedrol committed Nov 9, 2023
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  2. add test for unstable snapshot

    @mirpedrol
    mirpedrol committed Nov 9, 2023
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  3. don't assert run() function from snapshot generator

    @mirpedrol
    mirpedrol committed Nov 9, 2023
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  4. Update tests/components/create_snapshot.py 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @mirpedrol @mashehu
    mirpedrol and mashehu authored Nov 9, 2023
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Commits on Nov 13, 2023

  1. add linting code for environemnt.yml

    @mashehu
    mashehu committed Nov 13, 2023
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  2. add hint for language server, update to new new for schema file

    @mashehu
    mashehu committed Nov 13, 2023
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  3. add types

    @mashehu
    mashehu committed Nov 13, 2023
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  4. add schema based validation to environment yaml linting, add tests

    @mashehu
    mashehu committed Nov 13, 2023
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  5. Merge branch 'dev' into migrate-component-create-to-nf_test

    @mashehu
    mashehu authored Nov 13, 2023
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  6. fix mypy

    @mashehu
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  7. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 13, 2023
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  8. fix type error

    @mashehu
    mashehu committed Nov 13, 2023
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  9. add nf-test dependency

    @mashehu
    mashehu committed Nov 13, 2023
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  10. install nf-test for ci

    @mashehu
    mashehu committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. switch bump_version to use environemt.yml

    @mashehu
    mashehu committed Nov 14, 2023
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  2. update modules in pipeline template

    @mashehu
    mashehu committed Nov 14, 2023
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  3. fix test for updated snapshot

    @mashehu
    mashehu committed Nov 14, 2023
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  4. test for name mismatch in environment.yml

    @mashehu
    mashehu committed Nov 14, 2023
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  5. make nicer diff for nf-test error

    @mashehu
    mashehu committed Nov 14, 2023
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  6. fix error in download test

    @mashehu
    mashehu committed Nov 14, 2023
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  7. don't convert arrays to strings in licence field

    @mashehu
    mashehu committed Nov 14, 2023
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  8. add nf-test to CI

    @mashehu
    mashehu committed Nov 14, 2023
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  9. fix environment.yml linting

    @mashehu
    mashehu committed Nov 14, 2023
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  10. rely on environment.yml for bioconda versions

    @mashehu
    mashehu committed Nov 14, 2023
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  11. fix tests

    @mashehu
    mashehu committed Nov 14, 2023
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  12. fix types

    @mashehu
    mashehu committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. remove subworkflows test_yml_builder and fix subworkflow tests

    @mirpedrol
    mirpedrol committed Nov 15, 2023
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  2. fix nf-test setup in CI

    @mashehu
    mashehu committed Nov 15, 2023
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  3. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 15, 2023
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  4. fix assertion value

    @mashehu
    mashehu committed Nov 15, 2023
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  5. handle local modules without nf-test

    @mashehu
    mashehu committed Nov 15, 2023
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  6. add linting for nf-test and remove linting for pytests

    @mirpedrol
    mirpedrol committed Nov 15, 2023
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  7. fix linting components errors

    @mirpedrol
    mirpedrol committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. remove tmp dir manually if we find a PermissionError

    @mirpedrol
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  2. fix launch tests, move tmp pipeline creation to utils to share betwee… 

    …n tests

add types to utils
    @mashehu
    mashehu committed Nov 16, 2023
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  3. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
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  4. fix tests by correcting raised error type

    @mashehu
    mashehu committed Nov 16, 2023
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  5. fix tests, switch to pdiff instead of icdiff, because it handles widt… 

    …h better
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  6. revert e19a4a2

    @mirpedrol
    mirpedrol committed Nov 16, 2023
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  7. Apply suggestions from code review 

    Co-authored-by: Júlia Mir Pedrol <[email protected]>
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    mashehu and mirpedrol authored Nov 16, 2023
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  8. remove debugging raise introduced by mistake

    @mirpedrol
    mirpedrol committed Nov 16, 2023
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Commits on Nov 20, 2023

  1. move create-snapshot command to test command

    @mirpedrol
    mirpedrol committed Nov 20, 2023
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  2. move modules and subworkflows test tests to components

    @mirpedrol
    mirpedrol committed Nov 20, 2023
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  3. add test for generate snapshot once

    @mirpedrol
    mirpedrol committed Nov 20, 2023
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  4. update README

    @mashehu
    mashehu committed Nov 20, 2023
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  5. Apply suggestions from code review 

    Co-authored-by: Júlia Mir Pedrol <[email protected]>
    @mashehu @mirpedrol
    mashehu and mirpedrol authored Nov 20, 2023
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  6. fix typing errors

    @mashehu
    mashehu committed Nov 20, 2023
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  7. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
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  8. remove last traces of create-snapshot or create-test-yml

    @mashehu
    mashehu committed Nov 20, 2023
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  9. fix parameters

    @mashehu
    mashehu committed Nov 20, 2023
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  10. update changelog

    @mashehu
    mashehu committed Nov 20, 2023
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  11. rename create_snapshot functions and files

    @mashehu
    mashehu committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. simplify obsolete check

    @mashehu
    mashehu committed Nov 21, 2023
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  2. add back option to handle pytest based modules in bump_version

    @mashehu
    mashehu committed Nov 21, 2023
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  3. rename generator to test to make it hopefully less confusing

    @mashehu
    mashehu committed Nov 21, 2023
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  4. automatically sort dependencies in environment.yml while linting

    @mashehu
    mashehu committed Nov 21, 2023
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  5. fix types

    @mashehu
    mashehu committed Nov 21, 2023
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  6. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 21, 2023
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  7. fix typo

    @mashehu
    mashehu committed Nov 21, 2023
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  8. fix import statement

    @mashehu
    mashehu committed Nov 21, 2023
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  9. Update nf_core/components/components_test.py

    @mashehu
    mashehu authored Nov 21, 2023
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  10. remove self.run_tests

    @mashehu
    mashehu committed Nov 21, 2023
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  11. Merge branch 'migrate-component-create-to-nf_test' of github.com:mash… 

    …ehu/tools into migrate-component-create-to-nf_test
    @mashehu
    mashehu committed Nov 21, 2023
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