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@bentsherman bentsherman commented Nov 15, 2025

This PR adds several features to facilitate pipeline chaining based on workflow inputs/outputs

  • Allow a collection param to be loaded from a CSV / JSON / YAML file
  • Print JSON representation of workflow outputs at end of run
  • Allow JSON params to be supplied via stdin ?
  • Allow code snippets to implicitly declare params and outputs ?

Demo project: bentsherman/pipeline-chaining-demo

The JSON output is very similar to the lineage record (lid://<workflow-run-hash>#output), so maybe we could use that instead. The lineage record has the advantage of using LIDs for files, but the JSON structure doesn't quite match the params file.

With a bit more magic we could even make the pipeline chain as simple as a Bash pipeline:

# print only output JSON to stdout when params are supplied via stdin
cat params.json | nf run fetchngs | nf run rnaseq --transcriptome [...]

But the main thing for now is the basic reading/writing of inputs/outputs, then enhanced validation with schemas and record types.

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2 participants