Add table renderer with terraform-docs-style output and marker injection

[adamrtalbot]

Summary

Add a new table output format that generates compact Markdown tables, inspired by terraform-docs and related to nextflow-io/nf-schema#201.

Changes

• New TableRenderer (src/nf_docs/renderers/table.py) — generates terraform-docs-style dense Markdown tables with sections for Inputs (grouped), Configuration, Workflows (with calls), Processes (with I/O sub-tables), and Functions
• Marker-based injection — supports <!-- BEGIN_NF_DOCS --> / <!-- END_NF_DOCS --> markers for embedding generated docs into an existing README without overwriting surrounding content
• CLI integration — nf-docs generate . -f table writes a README.md to the output directory
• 47 renderer tests (10 for marker injection, 12 for table rendering, 25 existing unchanged)

Marker injection

When the output README.md already exists and contains the markers:

# My Pipeline

Some custom intro text.

<!-- BEGIN_NF_DOCS -->
(auto-generated content replaced here)
<!-- END_NF_DOCS -->

Custom footer text preserved.

Running nf-docs generate . -f table -o . will replace only the content between the markers, preserving everything else. If no markers exist, the file is created with markers wrapping the content.

Example output

# my-pipeline

**Version:** 1.0.0 · A pipeline for analysis

## Inputs

### Input/output

| Name | Description | Type | Default | Required |
|------|-------------|------|---------|:--------:|
| `--input` | Path to input | `string` | n/a | yes |
| `--outdir` | Output directory | `string` | `./results` | no |

## Processes

| Name | Description |
|------|-------------|
| `FASTQC` | Run FastQC on input reads |
| `MULTIQC` | Aggregate QC reports |

[ewels]

LGTM, thanks!

[ewels]

Inputs, not params / parameters?

[ewels]

Ah, ok - to match outputs below. Fair enough.

[adamrtalbot]

I've added selective items, so you can do this:

<!-- BEGIN_NF_DOCS -->
{{ inputs }}
{{ config }} 
<!-- END_NF_DOCS -->

And discard everything else. This could be useful for adding high level docs for a README.md

[ewels]

I didn't have push permissions to your fork, so I just merged. But see main for a couple of commits I added on at the end.