Nextflow pipeline to downsample sequences from GISAID

• Download unmasked alignment and genomic epidemiology metadata from GISAID
• Edit bin/downsample_metadata.py and bin/downsample_sd_data.py as per requirements
• Edit config_nf.txt as per requirements
• ./start_docker.sh -> Mount docker container and associated volumes. See script for more details
• chmod +x /code/bin/* -> Make all external scripts executable
• nextflow -C config_nf.txt run generate_guide_tree.nf to generate guide trees
• Nextflow workflows,
  • generate_guide_tree.nf to generate initial guide trees
  • generate_guide_tree_after_check.nf to generate rooted guide trees after manual checks
  • generate_xml.nf to generate XML from template from rooted guide trees
  • generate_xml_discrete.nf to get consensus trees, downsample trees from posterior and generate empirical discrete state XML from template
  • TODO: Write workflow to get consensus trees after discrete state analysis
  • run_persistence.nf to run persistence summarizer on trees from posterior annotated with complete jump history

Note: No workflow to run BEAST since versions might differ.