nf-core / nf-core/tools

Launch pipeline gives String instead of Number

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bug
Dominant language
Python
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322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
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Description

Description of the bug

Not sure what the cause is for this so it this report might not be on the correct repo. I tried the online launch feature on the website for the mag-pipeline. For one of the paramters, the "max_unbinned_contigs", the output params.json puts the integer inside quotes:

{
    "min_length_unbinned_contigs": 100000,
    "max_unbinned_contigs": "0",
    "binqc_tool": "checkm"
}

this results in an error when running the pipeline:

ERROR: Validation of pipeline parameters failed!


* --max_unbinned_contigs: expected type: Number, found: String (0)

The html field seems to be aware that it's a number so not sure where the error occurs.

Command used and terminal output

No response

System information

No response

Contributor guide

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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 online launch feature that generates params.json and trace how the max_unbinned_contigs value is serialized. Compare it with min_length_unbinned_contigs and verify the generated parameters pass pipeline validation with max_unbinned_contigs represented as a number rather than a quoted string.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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