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Using nf-core schema docs truncates `help_text´ #2865

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kedhammar opened this issue Mar 18, 2024 · 3 comments
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Using nf-core schema docs truncates `help_text´ #2865

kedhammar opened this issue Mar 18, 2024 · 3 comments
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@kedhammar
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Description of the bug

When using nf-core schema docs the output often truncates the help_text present in the original .json schema.

Command used and terminal output

nf-core schema docs > docs.md

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.13.1 - https://nf-co.recat docs.md


# nf-core/rnaseq pipeline parameters

RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.

## Input/output options

Define where the pipeline should find input data and save output data.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the
| `outdir` | The output directory where the results will be saved. You have to use absolute paths 

...
See truncated text above.

System information

No response

@kedhammar kedhammar added the bug Something isn't working label Mar 18, 2024
@awgymer
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awgymer commented Mar 19, 2024

Ok. This looks to be an issue with printing to console.

If you use the actual --output parameter you should see the full docs?

nf-core schema docs -o params.md

@awgymer
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awgymer commented Mar 19, 2024

I think this is a rich.console issue with cropping

@awgymer
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awgymer commented Mar 19, 2024

I've opened an issue on the rich GitHub to hopefully see if there is any way to fix the console printing.

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