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Support modules with exec: blocks #3633

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Support modules with exec: blocks #3633

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@muffato muffato commented Jun 20, 2025

With the current version, linting a module that has an exec: block yields the following error

╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                      ╷                          ╷                            │
│ Module name          │ File path                │ Test message               │
│╶─────────────────────┼──────────────────────────┼───────────────────────────╴│
│ hiccramalign/chunks  │ modules/sanger-tol/hicc… │ when: condition has too    │
│                      │                          │ many lines                 │
│                      ╵                          ╵                            │
╰──────────────────────────────────────────────────────────────────────────────╯

This is because the parser is not aware of exec: blocks.

In this PR I simply add code to recognise exec: blocks and check that they don't exist together with script: or shell:

Best,
Matthieu

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 Jun 20, 2025

Codecov Report

Attention: Patch coverage is 50.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 76.73%. Comparing base (7e944da) to head (6975c28).

Files with missing lines Patch % Lines
nf_core/modules/lint/main_nf.py 50.00% 4 Missing ⚠️

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@muffato @nf-core-bot
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