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formbio / laava

LAAVA: Long-read AAV Analysis
MIT License
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Feature request: more annotation in final report #12

Open krobison13 opened 6 months ago

krobison13 commented 6 months ago

It would be useful to embed more annotation in the final report to capture what sequences were used and perhaps some user-supplied descriptive text e.g. A listing of the annotation.txt as a table A possible command line argument pointing to a Markdown file to be incorporated as a page in the results

etal commented 6 months ago

Great ideas. It might be best to treat these as two separate feature requests.

krobison13 commented 6 months ago

You are leaping to conclusions if you think I have a well thought out use case :-)

Seriously, having an ability to include in the report a summary of experimental details, key internal identifiers such as batch numbers, experiment numbers, sample ids from a LIMS, project codes, etc.

I don't know what the PDF generation package is capable of, but being able to add headers/footers could be valuable - e.g. "INTERNAL USE ONLY" or "PROPRIETARY"

Going from the non-standard annotation format to something standard is a great idea.

On Tue, May 14, 2024 at 11:45 PM Eric Talevich @.***> wrote:

Great ideas. It might be best to treat these as two separate feature requests.

  • If we replace the bespoke annotation.txt format with standard BED for the vector and get the rest of the info from the BAM header, then the BED contents would be easy to display as a table in the report.
  • User-provided Markdown sounds good. Would you want that on the first page, below the preamble (title, date, sample ID)? Could you tell me more about your use cases?

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