4.62. sarscov2_lineages

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

4.62.1. Inputs

4.62.1.1. Required inputs

sarscov2_lineages.genome_fasta
File — Default: None
???

4.62.1.2. Other inputs

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

sarscov2_lineages.nextclade_one_sample.disk_size
Int — Default: 50
???

sarscov2_lineages.nextclade_one_sample.docker
String — Default: "nextstrain/nextclade:2.12.0"
???

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.nextclade_one_sample.virus_properties
File? — Default: None
???

sarscov2_lineages.pangolin_one_sample.analysis_mode
String? — Default: None
???

sarscov2_lineages.pangolin_one_sample.docker
String — Default: "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
???

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

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

sarscov2_lineages.pangolin_one_sample.update_dbs_now
Boolean — Default: false
???

4.62.2. Outputs

sarscov2_lineages.nextclade_aa_dels
String
???

sarscov2_lineages.nextclade_aa_subs
String
???

sarscov2_lineages.nextclade_clade
String
???

sarscov2_lineages.nextclade_json
File
???

sarscov2_lineages.nextclade_tsv
File
???

sarscov2_lineages.nextclade_version
String
???

sarscov2_lineages.pango_lineage
String
???

sarscov2_lineages.pango_lineage_report
File
???

sarscov2_lineages.pangolin_conflicts
String
???

sarscov2_lineages.pangolin_docker
String
???

sarscov2_lineages.pangolin_notes
String
???

sarscov2_lineages.pangolin_versions
String
???

sarscov2_lineages.scorpio_call
String
???

sarscov2_lineages.scorpio_notes
String
???


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