3. WDL Workflows

Documentation for each workflow is provided here. Although there are many workflows that serve different functions, some of the primary workflows we use most often include:

• demux_plus (on every sequencing run)
• classify_krakenuniq (included in demux_plus)
• assemble_denovo (for most viruses)
• assemble_refbased (for less diverse viruses, such as those from single point source human outbreaks)
• build_augur_tree (for nextstrain-based visualization of phylogeny)

• 3.1. align_and_count_report
  • 3.1.1. Inputs
    • 3.1.1.1. Required inputs
    • 3.1.1.2. Other inputs
• 3.2. align_and_plot
  • 3.2.1. Inputs
    • 3.2.1.1. Required inputs
    • 3.2.1.2. Other inputs
• 3.3. assemble_denovo
  • 3.3.1. Inputs
    • 3.3.1.1. Required inputs
    • 3.3.1.2. Other inputs
• 3.4. assemble_refbased
  • 3.4.1. Inputs
    • 3.4.1.1. Required inputs
    • 3.4.1.2. Other inputs
• 3.5. bams_multiqc
  • 3.5.1. Inputs
    • 3.5.1.1. Required inputs
    • 3.5.1.2. Other inputs
• 3.6. build_augur_tree
  • 3.6.1. Inputs
    • 3.6.1.1. Required inputs
    • 3.6.1.2. Other inputs
• 3.7. classify_kaiju
  • 3.7.1. Inputs
    • 3.7.1.1. Required inputs
    • 3.7.1.2. Other inputs
• 3.8. classify_krakenuniq
  • 3.8.1. Inputs
    • 3.8.1.1. Required inputs
    • 3.8.1.2. Other inputs
• 3.9. contigs
  • 3.9.1. Inputs
    • 3.9.1.1. Required inputs
    • 3.9.1.2. Other inputs
• 3.10. coverage_table
  • 3.10.1. Inputs
    • 3.10.1.1. Required inputs
    • 3.10.1.2. Other inputs
• 3.11. demux_metag
  • 3.11.1. Inputs
    • 3.11.1.1. Required inputs
    • 3.11.1.2. Other inputs
• 3.12. demux_only
  • 3.12.1. Inputs
    • 3.12.1.1. Required inputs
    • 3.12.1.2. Other inputs
• 3.13. demux_plus
  • 3.13.1. Inputs
    • 3.13.1.1. Required inputs
    • 3.13.1.2. Other inputs
• 3.14. deplete_only
  • 3.14.1. Inputs
    • 3.14.1.1. Required inputs
    • 3.14.1.2. Other inputs
• 3.15. downsample
  • 3.15.1. Inputs
    • 3.15.1.1. Required inputs
    • 3.15.1.2. Other inputs
• 3.16. fastq_to_ubam
  • 3.16.1. Inputs
    • 3.16.1.1. Required inputs
    • 3.16.1.2. Other inputs
• 3.17. fetch_annotations
  • 3.17.1. Inputs
    • 3.17.1.1. Required inputs
    • 3.17.1.2. Other inputs
• 3.18. multi_Fetch_SRA_to_BAM
  • 3.18.1. Inputs
    • 3.18.1.1. Required inputs
    • 3.18.1.2. Other inputs
• 3.19. filter_classified_bam_to_taxa
  • 3.19.1. Inputs
    • 3.19.1.1. Required inputs
    • 3.19.1.2. Other inputs
• 3.20. genbank
  • 3.20.1. Inputs
    • 3.20.1.1. Required inputs
    • 3.20.1.2. Other inputs
• 3.21. isnvs_merge_to_vcf
  • 3.21.1. Inputs
    • 3.21.1.1. Required inputs
    • 3.21.1.2. Other inputs
• 3.22. isnvs_one_sample
  • 3.22.1. Inputs
    • 3.22.1.1. Required inputs
    • 3.22.1.2. Other inputs
• 3.23. mafft
  • 3.23.1. Inputs
    • 3.23.1.1. Required inputs
    • 3.23.1.2. Other inputs
• 3.24. mafft_and_trim
  • 3.24.1. Inputs
    • 3.24.1.1. Required inputs
    • 3.24.1.2. Other inputs
• 3.25. merge_bams
  • 3.25.1. Inputs
    • 3.25.1.1. Required inputs
    • 3.25.1.2. Other inputs
• 3.26. merge_metagenomics
  • 3.26.1. Inputs
    • 3.26.1.1. Required inputs
    • 3.26.1.2. Other inputs
• 3.27. merge_tar_chunks
  • 3.27.1. Inputs
    • 3.27.1.1. Required inputs
    • 3.27.1.2. Other inputs
• 3.28. multiqc_only
  • 3.28.1. Inputs
    • 3.28.1.1. Other inputs
• 3.29. scaffold_and_refine
  • 3.29.1. Inputs
    • 3.29.1.1. Required inputs
    • 3.29.1.2. Other inputs
• 3.30. trimal
  • 3.30.1. Inputs
    • 3.30.1.1. Required inputs
    • 3.30.1.2. Other inputs