Simplify CI workflows and remove nf-core specific checks - #121
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FloWuenne merged 1 commit intoApr 13, 2026
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Fixes for the two real CI failures on this branch: - Reformat modules/local/AGENTS.md to satisfy prettier (pipe-table trailing whitespace). - Update utils_nf_aggregate subworkflow snapshot to drop removed 'fusion' field from parsed samplesheet meta. Workflow cleanup, consistent with the removal of MultiQC / Gantt / SEQERA_RUNS_DUMP in this PR: - Drop branch.yml (enforces nf-core dev-branch PR convention not used by this repo). - Drop fix-linting.yml (depends on nf-core-bot token/comments). - Drop template_version_comment.yml (nags about nf-core template version; low-value for a seqeralabs-branded pipeline). - Drop linting_comment.yml (only useful as companion to the nf-core pipelines lint job, which is also dropped). - Drop download_pipeline.yml (tests 'nf-core pipelines download', unused install path and 'ci' is already in skip_features). - Simplify linting.yml to just run pre-commit (drop the nf-core pipelines lint job — this is a seqeralabs pipeline, is_nfcore:false, and the lint job was currently red). Housekeeping: - Delete dangling assets/multiqc_config.yml (no longer referenced anywhere after MultiQC removal).
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Description
This PR removes several nf-core-specific GitHub Actions workflows and simplifies the linting workflow to focus on code formatting only. The changes reflect a shift away from nf-core pipeline conventions toward a more independent project structure.
Changes Made
Removed workflows:
download_pipeline.yml- Pipeline download testing workflowfix-linting.yml- Automated linting fix workflow triggered by commentsbranch.yml- Branch protection workflow enforcing dev branch PRstemplate_version_comment.yml- nf-core template version checkinglinting_comment.yml- Automated linting results comment postingModified
linting.yml:nf-corejob that rannf-core pipelines lintpre-commitjob for code formatting validationMinor formatting fixes:
multiqc_config.yml(no longer needed)modules/local/AGENTS.mdRationale
These changes align the project with its independent status, removing dependencies on nf-core tooling and conventions. The simplified linting workflow maintains code quality through pre-commit checks while removing nf-core-specific validation steps.
PR Checklist
https://claude.ai/code/session_012Dks8jvRprxGta93t4o72Q