Currently seqerakit does support dataset creation but to have an e2e flow where a pipeline input can reference a Seqera Platform's dataset url is necessary to use a mix of python and yaml.
It would be great to have the possibility to define in the same yaml a forward reference for entities created at different stage of the execution:
Pseudo-code
dataset:
name: 'input.csv'
file: 'samplesheet/rnaseq.csv'
reference: 'my-input'
...
pipeline:
name: rnaseq
...
launch:
pipeline:
name: rnaseq
params:
input: $ref.my-input <- that's references the url of the previously created dataset
The behavioud could also be enforced with validation where the $ref keyword (or similar) can be parsed to check if in the timeline of the execution an entity with that name has been created.
Once available, the same can be used for data-links
Currently seqerakit does support dataset creation but to have an e2e flow where a pipeline input can reference a Seqera Platform's dataset url is necessary to use a mix of python and yaml.
It would be great to have the possibility to define in the same yaml a forward reference for entities created at different stage of the execution:
Pseudo-code
The behavioud could also be enforced with validation where the $ref keyword (or similar) can be parsed to check if in the timeline of the execution an entity with that name has been created.
Once available, the same can be used for data-links