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Forward reference dataset and retrieve URL for input params #134

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@ejseqera ejseqera commented Apr 5, 2024

Re #116

Testing out functionality to retrieve the dataset URL referencing a dataset name using YAML anchor and provide URL as input param in params-file.

To test:

datasets:
  - name: &dataset 'test-sqkit-dataset'
    file-path: './examples/yaml/datasets/rnaseq_samples.csv'
    description: 'My test dataset'
    workspace: 'scidev/testing'
    overwrite: True
launch:
  - name: "nf-core-rnaseq"
    pipeline: "nf-core-rnaseq"
    workspace: 'scidev/testing'
    params:
      input: *dataset 

This YAML creates a dataset, where the name is used as an anchor and the alias is referenced in the params block. The utils.update_dataset_params() method will retrieve the appropriate URL for the dataset to be used when launching a pipeline, or adding it to the Launchpad.

TODO:

  • Add docs on usage
  • Add tests

@ejseqera ejseqera changed the base branch from main to dev April 5, 2024 23:28
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