nextflow-io / nextflow-io/nf-schema
Warning message being created with nested parameters
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- Dominant language
- Groovy
- Stars
- 57
- Forks
- 31
- Avg merge
- 3d 17h
- Merged PRs (30d)
- 1
Description
The parameters excluded from the main --help message are being flagged as invalid input values during runtime.
Context:
The parameters intended for the main help message are defined using categories in the $defs section.
The parameters intended for the --helpFull message are nested. These nested parameters are being flagged as invalid input values.
Warning message when pipeline is run (without the --help flag)
WARN: The following invalid input values have been detected:
* --repeat_library: /home/ramsivakumar/tostadas-workdir/tostadas/assets/lib/mpxv_repeats_lib.fasta
* --bakta_output_dir: bakta_outputs
* --final_liftoff_output_dir: liftoff_outputs
* --bakta_db_type: light
* --bakta_min_contig_length: 200
* --bakta_threads: 2
* --bakta_gram: ?
* --bakta_genus: Genus
Question: How do I remove this warning message?
Contributor guide
No contributing guide indexed for this repository
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 by reproducing the warning with the nested parameters described under the schema's $defs section, using a pipeline run without --help. Trace how those nested parameters are classified during runtime validation, then confirm the warning no longer lists valid nested values while genuinely invalid inputs are still reported.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100