4. WDL WorkflowsΒΆ
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_multi (metagenomics & host depletion)
- assemble_denovo (for most viruses)
- assemble_refbased (for less diverse viruses, such as those from single point source human outbreaks)
- augur_from_assemblies (for nextstrain-based visualization of phylogeny)
- genbank (for NCBI Genbank submission)
- 4.1. align_and_count_report
- 4.2. align_and_count_multiple_report
- 4.3. align_and_plot
- 4.4. assemble_denovo
- 4.5. assemble_refbased
- 4.6. augur_from_assemblies
- 4.7. augur_from_beast_mcc
- 4.8. augur_from_msa
- 4.9. augur_from_newick
- 4.10. bams_multiqc
- 4.11. beast_gpu
- 4.12. classify_kaiju
- 4.13. classify_kraken2
- 4.14. classify_krakenuniq
- 4.15. classify_multi
- 4.16. classify_single
- 4.17. contigs
- 4.18. coverage_table
- 4.19. demux_metag
- 4.20. demux_only
- 4.21. demux_plus
- 4.22. deplete_only
- 4.23. diff_genome_sets
- 4.24. downsample
- 4.25. fastq_to_ubam
- 4.26. fetch_annotations
- 4.27. multi_Fetch_SRA_to_BAM
- 4.28. filter_classified_bam_to_taxa
- 4.29. filter_sequences
- 4.30. genbank
- 4.31. isnvs_merge_to_vcf
- 4.32. isnvs_one_sample
- 4.33. kraken2_build
- 4.34. mafft
- 4.35. mafft_and_snp
- 4.36. mafft_and_trim
- 4.37. merge_bams
- 4.38. merge_metagenomics
- 4.39. merge_tar_chunks
- 4.40. merge_vcfs
- 4.41. merge_vcfs_and_annotate
- 4.42. multiqc_only
- 4.43. scaffold_and_refine
- 4.44. subsample_by_metadata
- 4.45. trimal