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fix: restore mamba-org/setup-micromamba in CI#33

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cokelaer merged 1 commit intomainfrom
copilot/fix-ci-failure
Apr 1, 2026
Merged

fix: restore mamba-org/setup-micromamba in CI#33
cokelaer merged 1 commit intomainfrom
copilot/fix-ci-failure

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Copilot AI commented Apr 1, 2026

PR #32 accidentally replaced mamba-org/setup-micromamba@v1 with actions/setup-python@v5. The latter silently ignores conda-specific parameters (environment-file, micromamba-version, etc.), so none of the bioinformatics tools defined in environment.yml (fastp, bowtie2, samtools, macs3, …) were ever installed — causing fastp to exit with code 127 and the full pipeline test to fail.

Changes

  • .github/workflows/main.yml: revert setup step back to mamba-org/setup-micromamba@v1, restoring conda environment installation from environment.yml

@cokelaer cokelaer marked this pull request as ready for review April 1, 2026 21:49
@cokelaer cokelaer merged commit 5ceec52 into main Apr 1, 2026
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2 participants