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Fix nextflow pipeline config lookup#277

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sjh9714 wants to merge 1 commit into
anthropics:mainfrom
sjh9714:fix-nextflow-pipeline-config-path
Closed

Fix nextflow pipeline config lookup#277
sjh9714 wants to merge 1 commit into
anthropics:mainfrom
sjh9714:fix-nextflow-pipeline-config-path

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@sjh9714

@sjh9714 sjh9714 commented May 28, 2026

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Summary

Fixes #187.

load_pipeline_config() was walking one directory too far up from scripts/utils/validators.py, so it looked for pipeline YAML files under nextflow-development/config/pipelines instead of nextflow-development/scripts/config/pipelines. This updates the lookup to the actual scripts config directory so known pipelines such as rnaseq load correctly.

Changes

  • Point the validator config lookup at scripts/config/pipelines.
  • Add focused unittest coverage for known and unknown pipeline config loading, plus the validator path that previously reported a known pipeline as unknown.

Testing

  • PYTHONDONTWRITEBYTECODE=1 /tmp/kwork-venv/bin/python -m unittest discover -s bio-research/skills/nextflow-development/scripts/tests

I also ran the same regression assertion against an unmodified checkout before the fix and confirmed it failed because load_pipeline_config("rnaseq") returned None.

Note: I used Codex while preparing this change, reviewed the final diff, and ran the listed checks locally.

@bryan-anthropic

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Pipeline config lookup points to the wrong folder for known pipelines

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