fix: combined runtime - #128
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Not perfect but here's where we're at |
- Auto-format markdown/json files via prettier hook - Fix editorconfig indentation in main.nf (line 36: 4-space multiple alignment) Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
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The Agent quick verify sequence was missing the pre-commit lint step, causing agents to push unformatted files that fail the CI prettier hook. Add it as step 4 with guidance on handling auto-fixed files. Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
…branch The nf-core job reads nf_core_version from .nf-core.yml via pietrobolcato/action-read-yaml, but the file was removed from dev. This produces 'pip install nf-core==' (empty version) which fails. Port the fix from dev (e484e8a): remove the entire nf-core job, keeping only the pre-commit job. Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
adamrtalbot/detect-nf-test-changes@v0.0.3 parses include lines with line.split()[2] and crashes on multi-line include blocks (IndexError). Port the fix from dev (cfa47bf): collapse multi-line include blocks into single-line format. Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
…-core.yml Prevent agents from reintroducing multi-line include blocks in main.nf or re-adding the nf-core lint job without .nf-core.yml. Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
fix: resolve pre-commit lint errors (prettier + editorconfig)
FloWuenne
approved these changes
Apr 20, 2026
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).