Allow collection-type params to be loaded from files#6675
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bentsherman merged 2 commits intomasterfrom Dec 19, 2025
Merged
Allow collection-type params to be loaded from files#6675bentsherman merged 2 commits intomasterfrom
bentsherman merged 2 commits intomasterfrom
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christopher-hakkaart
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Dec 18, 2025
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Docs look good. No comments.
jorgee
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I have been testing with other standard library objects, and it is working with Set and List, but not with Bag, IterableandMap`.
- It is not possible to cast the
ArrayListobject returned by the slurpers to a Bag. I think it should be supported as in the documentation clearly says thatBagis aCollection. Iterableis a superinterface ofCollectionMapis not aCollection, but there is a direct mapping of YAML and JSON files with Maps.
Not sure if it was the goal of the PR to support all the types, but I see it is possible with very little changes. I have created #6676 to support all these types.
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Thanks Jorge. I intentionally did not support Iterable and Map because I'm not sure about those cases yet. But I did intend to support Bag so thank you for catching that |
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@pditommaso the bump of Netty version is producing failures in azure tests |
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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jorgee
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This PR adds the ability to declare a param as a collection type:
params { input: List<Map> } workflow { println params.input*.id.join(',') }And supply a CSV, JSON, or YAML file at runtime:
Nextflow interprets the string as a file path and attempts to load the file contents based on the file extension. A runtime error is reported if the file contents are not compatible with the declared type.
Future work will extend the type validation with record types.
(spun off from #6574)