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Feature/test datasets#3548

Merged
JulianFlesch merged 15 commits intonf-core:devfrom
JulianFlesch:feature/test-datasets
May 7, 2025
Merged

Feature/test datasets#3548
JulianFlesch merged 15 commits intonf-core:devfrom
JulianFlesch:feature/test-datasets

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@JulianFlesch JulianFlesch commented Apr 28, 2025 •
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This PR addresses usability improvements that were suggested by @ewels and @mashehu for the new test-datasets subcommand.
Changes:

  • Order of subcommands in nf-core -h changed
  • Help texts in nf-core test-datasets -h shortened
  • Optional query argument added to nf-core test-dataset search which pre-populates the autocomplete. If query is unambiguous, autocomplete is skipped.
  • Parameter --branch is attempted to be inferred from the current working dir to pre-populate the autocomplete

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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codecov Bot commented Apr 28, 2025 •
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Codecov Report

Attention: Patch coverage is 24.00000% with 19 lines in your changes missing coverage. Please review.

Project coverage is 76.48%. Comparing base (94c8eff) to head (10051de).
Report is 37 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/test_datasets/test_datasets_utils.py 14.28% 12 Missing ⚠️
nf_core/test_datasets/search.py 0.00% 5 Missing ⚠️
nf_core/__main__.py 75.00% 1 Missing ⚠️
nf_core/commands_test_datasets.py 50.00% 1 Missing ⚠️

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@ewels
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ewels commented Apr 29, 2025

Waiting for @mashehu to review (and @mirpedrol ?)

mashehu
mashehu approved these changes Apr 29, 2025
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Comment thread nf_core/__main__.py Outdated
Comment thread nf_core/test_datasets/search.py Outdated
Comment thread nf_core/test_datasets/search.py Outdated
@JulianFlesch
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JulianFlesch commented Apr 30, 2025

Can I merge this when tests have run @mashehu?

mirpedrol
mirpedrol approved these changes Apr 30, 2025
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Comment thread nf_core/__main__.py
@JulianFlesch JulianFlesch merged commit 742897d into nf-core:dev May 7, 2025
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@mashehu mashehu mashehu approved these changes

@mirpedrol mirpedrol mirpedrol approved these changes

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5 participants

@JulianFlesch @ewels @mashehu @mirpedrol @nf-core-bot