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Upgrade environment schema to support additional scenarios#11758

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biocorecrg:environment-schema
Open

Upgrade environment schema to support additional scenarios#11758
toniher wants to merge 2 commits into
nf-core:masterfrom
biocorecrg:environment-schema

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@toniher toniher commented May 25, 2026

The schema now accepts two additional scenarios for conda environment definitions:

  1. Bare pip dependency (5 lines added)

    • Allows specifying pip as a standalone string dependency
    • Enables pip-based installs in the environment
  2. Flexible pip package specifications (refactored pip packages validation)

    • Previously: only accepted version-pinned format (package==version)
    • Now accepts either:
      • Version-pinned packages: package==version (maintains reproducibility)
      • Direct URLs: http:// or https:// links to package artifacts (e.g., wheel files)

Motivation: GitHub issue #11652 — this expands the schema to handle more real-world dependency scenarios while preserving reproducibility where pinning is specified.


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@toniher toniher requested a review from mashehu May 25, 2026 14:49
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toniher commented Jun 1, 2026

Hey @mashehu , any feedback or further idea?

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