4.49. sarscov2_lineages¶

Call Nextclade and Pangolin lineages on a single SARS-CoV-2 genome

4.49.1. Inputs¶

sarscov2_lineages.genome_fasta
File — Default: None
???

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sarscov2_lineages.nextclade_one_sample.auspice_reference_tree_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.gene_annotations_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.pcr_primers_csv
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.qc_config_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.root_sequence
File? — Default: None
???

sarscov2_lineages.pangolin_one_sample.docker
String — Default: "staphb/pangolin:2.3.2-pangolearn-2021-02-21"
???

sarscov2_lineages.pangolin_one_sample.max_ambig
Float? — Default: None
???

sarscov2_lineages.pangolin_one_sample.min_length
Int? — Default: None
???

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