update pipeline level nf-test documentation #3115
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mashehu
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Feb 27, 2025
sites/docs/src/content/docs/guidelines/pipelines/recommendations/testing.md
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| - To ensure all output files are caught, the `params.outdir` should be set the the nf-test variable `outputDir` | ||
| - The tag `PIPELINE` and the pipeline name should be added to all tests | ||
| - To ensure all output files are caught, it is highly recommended to use the `nft-utils` plugin to parse the output of the pipeline. |
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that's the example that follows
sites/docs/src/content/docs/guidelines/pipelines/recommendations/testing.md
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sites/docs/src/content/docs/guidelines/pipelines/recommendations/testing.md
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| `stable_path` capture all of the stable files in the output directory, ignoring the files listed in the `.nftignore` file. | ||
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| Additional plugins can be used if files with unstable content can be read using a nf-test plugin. | ||
| For example for BAM and CRAM files the `nft-bam` plugin is used, while the `nft-vcf` plugin is also used, both in conjonction with `nft-utils`: |
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should we move this section into the nf-test assertion examples (and split it up into component tests and pipeline tests?
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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