feat: parsnp module#11196
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akaviaLab
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Apr 20, 2026
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In general, looks good to me, but I have some comments. I'd suggest getting one of the core maintainers to look at it.
famosab
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Apr 21, 2026
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Thank you for your contribution to nf-core! I added a few comments to your PR. :)
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I think you're not supposed to gave ontologies in the meta parts of a
tuple. AFAIK, the groovy maps don't need it.
Apart from that, looks good to me!
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On modules/nf-core/parsnp/meta.yml
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famosab
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Apr 22, 2026
famosab
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Few more comments, almost good to go :)
| "test.ggr:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "partition": [ |
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Is this supposed to be empty for this test?
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I've updated the tests to include a partition run and force output -- the deterministic md5s are included in the snapshot. I ran into errors using sanitizeOutput for this purpose so I use snapshot(...).match().
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i see, but then we still need to assert the partititon output because whats the point of the test otherwise ;)
| e.g. `[ id:'sample1' ]` | ||
| - "partition": | ||
| type: directory | ||
| description: Output directory from partition mode containing results of each partitioned run. Only present when --partition is specified. |
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can we add a --partition test then to see if this works? :)
famosab
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Apr 28, 2026
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It looks like you need to update nf-tools, and make sure you've merged the most recent master branch. A lot of the errors seems to be related to those kind of issues, so it is hard to tell what exactly is failing. |
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May 5, 2026
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| "test.ggr:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "partition": [ |
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i see, but then we still need to assert the partititon output because whats the point of the test otherwise ;)
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PR checklist
Closes #8614.
This PR adds a new
parsnpmodule and tests. The test is a bit contrived because I'm using the same FASTA files but I think it is sufficient -- I can also add some more complex test cases if preferred.topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda