nextflow-io / nextflow-io/nextflow

`nextflow launch` validate parameters prior to running pipeline

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stale
Dominant language
Groovy
Stars
3.5k
Forks
811
Avg merge
2d 11h
Merged PRs (30d)
61

Description

New feature

Currently, it is possible to run an invalid pipeline with nextflow launch

e.g. nextflow launch nf-core/rnaseq (no parameters!) will start and cause a large delay (high latency) before failing (required arguments, --input and --outdir).

Use case

Validate a pipeline early before sending to Seqera Platform.

Suggested implementation

It's not practical to run the contents of the pipeline really, but some early validation should be performed.

We could either:

  • Validate against the nextflow_schema.json or config options before sending to Platform
    • Will validate parameters early but can't do anything about invalid contents
  • Use -preview or nextflow inspect could be used internally to do run a mock pipeline
    • Will do a deeper check, but likely to trip up over authentication or access issues which will deviate from the remote compute environment
  • Validate on platform, return the yes or no signal back to Nextflow
    • More complicated, requires extensive engineering on both sides.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the nextflow launch command and its handoff to Seqera Platform; compare the suggested schema/config validation with -preview or nextflow inspect. Define which early checks are in scope and how a clear success or failure signal is returned before platform execution.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy
Domain
cli, cloud
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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