Add pipeline AGENTS.md - #2

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itrujnara merged 23 commits into

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Jul 1, 2026

Commits on Jun 15, 2026

AGENTS.md initial draft part 1
itrujnara
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6077050

Commits on Jun 16, 2026

AGENTS.md initial draft part 2
itrujnara
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3bb84d5
Add extra nf-test info to AGENTS.md
itrujnara
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08031a8
Apply suggestions from code review

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394f05d
Add some Nextflow pitfalls
itrujnara
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2499a94
Merge branch 'add-agents-md' of https://github.com/nf-core/agents into add-agents-md
itrujnara
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4d38f41
Apply complex suggestions from code review
itrujnara
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468c8ce

Commits on Jun 17, 2026

Reduce the pre-commit routine description
itrujnara
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82d1ed4
Apply straightforward comments from Evangelos
itrujnara
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5e4b500

Commits on Jun 18, 2026

Highlight command terms and remove redundant phrases
itrujnara
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1544869
Remove mention of patch branch
itrujnara
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a602e41
Rewrite from prose to bullets and reduce verbosity again
itrujnara
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bd32344

Commits on Jun 26, 2026

Apply suggestions from code review

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c43b634
Apply suggestions from code review

itrujnara
and
ewels
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d37dd76
Apply more complex suggestions from code review
itrujnara
committed
7027f86
Move definitions to top
itrujnara
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390c0ea
Rename AGENTS.md to resources/pipeline/AGENTS.md
itrujnara
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19d27c7

Commits on Jun 29, 2026

Apply suggestions from Arthur
itrujnara
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88b833f
Add note about treemap deviations
itrujnara
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2b6f5b8
Update resources/pipeline/AGENTS.md

itrujnara
and
pinin4fjords
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9a42400
Update resources/pipeline/AGENTS.md

itrujnara
and
pinin4fjords
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69b9e89
Convert config file section from description to instructions
itrujnara
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af52750
Revise treemap structure for clarity
itrujnara
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d594e3a