feat: Add markdown script for CNV report generation

[fevac]

This script is part of https://github.com/Clinical-Genomics/MTP-oncoflow/issues/34

Added

• Markdown script for CNV report generation, that takes two CNV tables (at gene and segment level) and creates a interactive report where those tables are searchable and sortable.

Notes

• This PR displays tables as-is. The report will need to be optimised once we know which values are relevant to display after assessing the verification cases.

• Standalone script usage:

Rscript -e "rmarkdown::render('cnv_report.Rmd', params = list(cnv_gene = 'path/to/cnv_gene.tsv', cnv_segment = 'path/to/cnv_segment.tsv'), output_file = 'cnv_report.html')"

[github-actions]

PR checklist

• Fill in description of the PR and link to any relevant issues.
• If you've fixed a bug, added a subworkflow or any other code that should be tested, add tests!
• If you've added a new tool, update citations according to the instructions under Adding Citations.
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• README.md is updated (including authors/contributors).

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[fevac]

Note: Changelog will be updated as part of parent issue

[beatrizsavinhas]

Even though the CI checks might fail, you should still be able to merge to your feature branch since it's not a protected branch! 😉

[fellen31]

Cool!

[fellen31]

Suggested change

	<summary><strong>How to use the yables (click to expand)</strong></summary>
	<summary><strong>How to use the tables (click to expand)</strong></summary>

[fellen31]

If this script is to be used within a module, I would put this script within the module: https://docs.seqera.io/nextflow/modules/developing-modules#resources 😊

[beatrizsavinhas]

I'm curious: How would this work if we were to use a shared module, like nf-co.re/modules/rmarkdownnotebook? 🤔
Do you have any idea @fellen31 ?

[fellen31]

Not sure...old way of doing things was to put all scripts in a shared ./bin/ folder.

[beatrizsavinhas]

Ah it seems that the module itself receives the path to the file as an input, so I guess it doesn't really matter where the file is located.

But otherwise, putting it in a shared ./bin/ directory would probably be the way to go since nextflow will automatically detect it there, as far as I understand!

[fellen31]

Well, it's only if the script is to be used within the script: block (and not as an input file). If it is actually an input, then I guess assets is fine.

[fellen31]

💯

[mathiasbio]

🌟

[kristinebilgrav]

Very nice!

[mathiasbio]

A small thing I noticed when looking at the example report was that the Gene column search was a little buggy. The filtering seemed to work but the searchbar didn't display the genename you search for. But maybe that can be addressed later!