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:

 - :doc:`demux_deplete` (on every sequencing run)
 - :doc:`classify_single` (metagenomics & host depletion)
 - :doc:`assemble_denovo` (for most viruses)
 - :doc:`assemble_refbased` (for less diverse viruses, such as those from single point source human outbreaks)
 - :doc:`augur_from_assemblies` (for nextstrain-based visualization of phylogeny)
 - :doc:`genbank` (for NCBI Genbank submission)

.. toctree::
   align_and_count
   align_and_count_multiple_report
   align_and_plot
   assemble_denovo
   assemble_refbased
   augur_export_only
   augur_from_assemblies
   augur_from_beast_mcc
   augur_from_mltree
   augur_from_msa
   augur_from_msa_with_subsampler
   bam_to_qiime
   bams_multiqc
   beast_gpu
   calc_bam_read_depths
   classify_kaiju
   classify_kraken2
   classify_krakenuniq
   classify_multi
   classify_qiime2_multi
   classify_single
   contigs
   coverage_table
   demux_deplete
   demux_metag
   demux_only
   demux_plus
   deplete_only
   detect_cross_contamination
   detect_cross_contamination_precalled_vcfs
   diff_genome_sets
   downsample
   fastq_to_ubam
   fetch_annotations
   fetch_sra_to_bam
   filter_classified_bam_to_taxa
   filter_sequences
   genbank
   isnvs_lofreq
   isnvs_merge_to_vcf
   isnvs_one_sample
   kraken2_build
   mafft
   mafft_and_snp
   mafft_and_snp_annotated
   mafft_and_trim
   merge_bams
   merge_metagenomics
   merge_tar_chunks
   merge_vcfs
   merge_vcfs_and_annotate
   metagenomic_denovo
   multiqc_only
   nextclade_single
   sarscov2_batch_relineage
   sarscov2_biosample_load
   sarscov2_data_release
   sarscov2_genbank
   sarscov2_genbank_ingest
   sarscov2_gisaid_ingest
   sarscov2_illumina_full
   sarscov2_lineages
   sarscov2_nextclade_multi
   sarscov2_nextstrain
   sarscov2_nextstrain_aligned_input
   sarscov2_sequencing_reports
   sarscov2_sra_to_genbank
   scaffold_and_refine
   subsample_by_casecounts
   subsample_by_metadata
   subsample_by_metadata_with_focal
   terra_table_to_tsv
   terra_update_assemblies
   trimal