Repository with the list of markdowns developed by our group for the different analyses:
- RNA-seq nextflow
- Bacterial Assembly nextflow
- Low Frequency Variants nextflow
- Viral Genome Assembly
- Bacterial assembly + snippy + canSNP
- Bacterial assembly + plasmidID
- Exome pipeline
To convert the .md file into a html file you must run the following command:
Rscript markdown_to_html.r <imput_markdown.md> <output_report.html>
Once you have generated your html file, if you want to create a PDF file of the report you must install 'wkhtmltopdf' package. Then you should run the following command.
wkhtmltopdf --keep-relative-links <input_html.html> <output_pdf.pdf>