Add AGENTS.md#12028
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pontus
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| main.nf **MUST** define one `process` with the following elements: | ||
| - Nextflow directives: | ||
| - `tag`: used for distinguishing processes in logs, usually set to "$meta.id" | ||
| - one or more `label`: used to set default resources | ||
| - `conda`: always set to "${moduleDir}/environment.yml" | ||
| - `container`: contains links to Docker and Singularity containers, gated by a fixed container engine check | ||
| - you **MUST NOT** add any other directives, they will be set by the pipeline | ||
| - Input section (`input:`): generally one tuple per logical entity (sample, reference, etc.) and `val` inputs for mandatory options; see https://nf-co.re/docs/specifications/components/modules/input-output-options for details | ||
| - Output section (`output:`): generally one output per logical file (e.g. one for sam/bam/cram and one for bai/crai); there must also be one topic output for each tool (to report the version); see https://nf-co.re/docs/specifications/components/modules/input-output-options for details | ||
| - `when:` section: you **MUST** leave the boilerplate intact | ||
| - Main script (`script:`): contains the shell script to execute, along with Nextflow code to generate the arguments; the definitions of `args` and `prefix` **MUST** be left intact | ||
| - Stub script (`stub`): contains a script to simulate the action of the module without running the tool | ||
| - All output file names **MUST** match the main script | ||
| - Compressed files **MUST** be generated by compressing an empty file | ||
| - The definitions of `args` and `prefix` **MUST** be left intact | ||
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can't we just point to the specifications and to use nf-core m lint, otherwise this will be a pain to keep in sync
pontus
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Jun 24, 2026
| └── nextflow.config // Nextflow configuration used for testing ONLY; multiple config files may exist in some cases | ||
| ``` | ||
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| ## Key terms |
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I don't think I know much about prompt engineering so my instincts may not be useful, but to a human reader, I think this terminology is better to have defined before they are used.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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This PR is part of the agent steering project (nf-core/proposals#143). It adds the initial version of AGENTS.md to facilitate AI-assisted development in this repository and increase submission quality.
The file is intended to provide basic guidance for agents working within the repository. It is not intended as a complete replacement for the component documentation or for the module developer agent skill. That said, I appreciate feedback on any missing basic information.
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