4.9. augur_from_mltree

Take a premade maximum likelihood tree (Newick format) and run the remainder of the augur pipeline (timetree modificaitons, ancestral inference, etc) and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/

4.9.1. Inputs

4.9.1.1. Required inputs

augur_from_mltree.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction

augur_from_mltree.genbank_gb
File — Default: None
A 'genbank' formatted gene annotation file that is used to calculate coding consequences of observed mutations. Must correspond to the same coordinate space as ref_fasta. Typically downloaded from the same NCBI accession number as ref_fasta.

augur_from_mltree.msa_or_vcf
File — Default: None
Multiple sequence alignment (aligned fasta) or variants (vcf format).

augur_from_mltree.raw_tree
File — Default: None
Maximum likelihood tree (newick format).

augur_from_mltree.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.

augur_from_mltree.sample_metadata
File — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details.

4.9.1.2. Other inputs

Show/Hide

augur_from_mltree.ancestral_traits.confidence
Boolean — Default: true
???

augur_from_mltree.ancestral_traits.disk_size
Int — Default: 750
???

augur_from_mltree.ancestral_traits.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.ancestral_traits.machine_mem_gb
Int — Default: 32
???

augur_from_mltree.ancestral_traits.sampling_bias_correction
Float? — Default: None
???

augur_from_mltree.ancestral_traits.weights
File? — Default: None
???

augur_from_mltree.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.

augur_from_mltree.ancestral_tree.disk_size
Int — Default: 300
???

augur_from_mltree.ancestral_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.ancestral_tree.infer_ambiguous
Boolean — Default: false
???

augur_from_mltree.ancestral_tree.inference
String — Default: "joint"
???

augur_from_mltree.ancestral_tree.keep_ambiguous
Boolean — Default: false
???

augur_from_mltree.ancestral_tree.keep_overhangs
Boolean — Default: false
???

augur_from_mltree.ancestral_tree.output_vcf
File? — Default: None
???

augur_from_mltree.ancestral_tree.vcf_reference
File? — Default: None
???

augur_from_mltree.assign_clades_to_nodes.disk_size
Int — Default: 300
???

augur_from_mltree.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades

augur_from_mltree.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_mltree.export_auspice_json.description_md
File? — Default: None
???

augur_from_mltree.export_auspice_json.disk_size
Int — Default: 300
???

augur_from_mltree.export_auspice_json.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.include_root_sequence
Boolean — Default: true
???

augur_from_mltree.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_mltree.export_auspice_json.machine_mem_gb
Int — Default: 64
???

augur_from_mltree.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.out_basename
String — Default: basename(basename(tree,".nwk"),"_timetree")
???

augur_from_mltree.export_auspice_json.title
String? — Default: None
???

augur_from_mltree.refine_augur_tree.branch_length_inference
String? — Default: None
???

augur_from_mltree.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???

augur_from_mltree.refine_augur_tree.clock_rate
Float? — Default: None
???

augur_from_mltree.refine_augur_tree.clock_std_dev
Float? — Default: None
???

augur_from_mltree.refine_augur_tree.coalescent
String? — Default: None
???

augur_from_mltree.refine_augur_tree.covariance
Boolean? — Default: None
???

augur_from_mltree.refine_augur_tree.date_confidence
Boolean — Default: true
???

augur_from_mltree.refine_augur_tree.date_inference
String? — Default: "marginal"
???

augur_from_mltree.refine_augur_tree.disk_size
Int — Default: 750
???

augur_from_mltree.refine_augur_tree.divergence_units
String? — Default: "mutations"
???

augur_from_mltree.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.refine_augur_tree.gen_per_year
Int? — Default: None
???

augur_from_mltree.refine_augur_tree.keep_polytomies
Boolean — Default: false
???

augur_from_mltree.refine_augur_tree.keep_root
Boolean — Default: true
???

augur_from_mltree.refine_augur_tree.machine_mem_gb
Int — Default: 75
???

augur_from_mltree.refine_augur_tree.precision
Int? — Default: None
???

augur_from_mltree.refine_augur_tree.root
String? — Default: None
???

augur_from_mltree.refine_augur_tree.vcf_reference
File? — Default: None
???

augur_from_mltree.translate_augur_tree.disk_size
Int — Default: 300
???

augur_from_mltree.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

augur_from_mltree.translate_augur_tree.genes
File? — Default: None
???

augur_from_mltree.translate_augur_tree.vcf_reference
File? — Default: None
???

augur_from_mltree.translate_augur_tree.vcf_reference_output
File? — Default: None
???

4.9.2. Outputs

augur_from_mltree.auspice_input_json
File
???

augur_from_mltree.time_tree
File
???

---

Generated using WDL AID (1.0.0)