Added nf-core/taxprofiler documentation and DSP About

[apalleja]

I added the taxprofiler documentation. It will need some fine-tunning (perhaps an update from the next time we use it), but at least now is there. I updated the index accordingly.

Also, I added some info about the Data Science paltform on the About.md.

[github-actions]

See the preview of the website at:

• https://biosustain.github.io/dsp_nfcore_documentation/pr-1/

[Copilot]

Pull request overview

Adds new documentation pages to the BRIGHT Nextflow pipeline docs site, covering nf-core/taxprofiler usage (including Azure/Seqera notes) and an “About” page describing the Data Science Platform.

Changes:

• Added a new taxprofiler/README.md documentation page with input formats, example commands, and captured run/config details.
• Updated index.md to include the new taxprofiler page in the docs navigation.
• Replaced the placeholder about.md with DSP background text and pillar descriptions.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 11 comments.

File	Description
taxprofiler/README.md	New taxprofiler documentation page with setup/run instructions and configuration excerpts.
index.md	Adds taxprofiler docs to the Sphinx toctree navigation.
about.md	Adds DSP overview content intended for the “About” section.

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[Copilot]

This introductory sentence is grammatically incorrect/awkward (“provide with a small manual to how to prepare, for running…”). Please rephrase to a clear instruction-focused sentence (e.g., that this page explains how to prepare inputs and run on Azure).

Suggested change

	Here we provide with a small manual to how to prepare, for running the pipeline and running it in the Microsoft Azure environment.
	This page provides step-by-step instructions for preparing inputs and running the pipeline in the Microsoft Azure environment.

[Copilot]

Minor grammar issues: “will be store” should be “will be stored”, and “were download” should be “were downloaded”.

Suggested change

	The databases will be store in the corresponding data lake folder called databases. Until then you have to download and prepare the databases yourself.
	Files for Metaphlan were download from:
	The databases will be stored in the corresponding data lake folder called databases. Until then you have to download and prepare the databases yourself.
	Files for Metaphlan were downloaded from:

[Copilot]

This line contains a user-specific absolute path and first-person phrasing (“/Users/... and I passed…”). For shared documentation, please replace with a generic placeholder path and instructions on how to locate the mOTUs DB directory in the environment, so it’s reproducible for other users.

[Copilot]

The embedded beforeText includes ANSI escape sequences (e.g., \x1b[0;32m...) which will render as garbage characters in the generated docs. Please strip ANSI codes (or capture the output with --monochrome_logs/equivalent) before committing this snippet.

[Copilot]

“# Worth noticing” introduces a second H1 in a page that already has an H1 at the top. Please demote this to an H2/H3 (and consider using a list) to keep the document structure consistent for Sphinx/Markdown rendering.

Suggested change

	# Worth noticing
	You need to add --shortread_qc_minlength 100 to require a minimum length for read after quality control
	You need to add --save_analysis_ready_fastqs to save the qc filetered reads before they go into classification or profiling
	You need to add --perform_runmerging to merge different lanes of the same sample
	You need to add --run_profile_standardisation so that all metaphlan profile of each sample get combined in a single report (This may be changed soon, follow issue: https://github.com/nf-core/taxprofiler/issues/494)
	## Worth noticing
	- You need to add `--shortread_qc_minlength 100` to require a minimum length for reads after quality control.
	- You need to add `--save_analysis_ready_fastqs` to save the QC-filtered reads before they go into classification or profiling.
	- You need to add `--perform_runmerging` to merge different lanes of the same sample.
	- You need to add `--run_profile_standardisation` so that all Metaphlan profiles of each sample get combined in a single report (this may be changed soon, follow issue: https://github.com/nf-core/taxprofiler/issues/494).

[Copilot]

The heading uses “Taxonomical”, which is nonstandard in this context; “Taxonomic profiling …” is the usual phrasing in bioinformatics/pipeline docs.

Suggested change

	## Taxonomical profiling using nf-core/taxprofiler pipeline
	## Taxonomic profiling using nf-core/taxprofiler pipeline

[enryH]

I updated links, paths and filenames. Shorted some lines and command to be not too long for displaying.