nextflow-io / nextflow-io/nextflow
`nextflow launch` validate parameters prior to running pipeline
Nobody has claimed this yet.
- 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
-previewornextflow inspectcould 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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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