3.6. build_augur_tree

3.6.1. Inputs

3.6.1.1. Required inputs

build_augur_tree.assembly_fastas
Array[File] — Default: None
???

build_augur_tree.export_auspice_json.auspice_config
File — Default: None
???

build_augur_tree.genbank_gb
File — Default: None
???

build_augur_tree.metadata
File — Default: None
???

build_augur_tree.ref_fasta
File — Default: None
???

build_augur_tree.virus
String — Default: None
???

3.6.1.2. Other inputs

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build_augur_tree.ancestral_tree.docker
String — Default: "nextstrain/base"
???

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

build_augur_tree.ancestral_tree.inference
String? — Default: None
???

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

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

build_augur_tree.ancestral_tree.machine_mem_gb
Int? — Default: None
???

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

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

build_augur_tree.augur_mafft_align.debug
Boolean? — Default: false
???

build_augur_tree.augur_mafft_align.docker
String — Default: "nextstrain/base"
???

build_augur_tree.augur_mafft_align.existing_alignment
Boolean? — Default: false
???

build_augur_tree.augur_mafft_align.fill_gaps
Boolean? — Default: true
???

build_augur_tree.augur_mafft_align.machine_mem_gb
Int? — Default: None
???

build_augur_tree.augur_mafft_align.remove_reference
Boolean? — Default: true
???

build_augur_tree.draft_augur_tree.docker
String — Default: "nextstrain/base"
???

build_augur_tree.draft_augur_tree.exclude_sites
File? — Default: None
???

build_augur_tree.draft_augur_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.draft_augur_tree.method
String? — Default: None
???

build_augur_tree.draft_augur_tree.substitution_model
String? — Default: None
???

build_augur_tree.draft_augur_tree.vcf_reference
File? — Default: None
???

build_augur_tree.export_auspice_json.docker
String — Default: "nextstrain/base"
???

build_augur_tree.export_auspice_json.machine_mem_gb
Int? — Default: None
???

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

build_augur_tree.refine_augur_tree.clock_filter_iqd
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.clock_rate
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.clock_std_dev
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.covariance
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.date_confidence
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.date_inference
String? — Default: None
???

build_augur_tree.refine_augur_tree.divergence_units
String? — Default: None
???

build_augur_tree.refine_augur_tree.docker
String — Default: "nextstrain/base"
???

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

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

build_augur_tree.refine_augur_tree.keep_root
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.refine_augur_tree.no_covariance
Boolean? — Default: false
???

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

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

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

build_augur_tree.translate_augur_tree.docker
String — Default: "nextstrain/base"
???

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

build_augur_tree.translate_augur_tree.machine_mem_gb
Int? — Default: None
???

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

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

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