4.46. subsample_by_metadata_with_focal

Filter and subsample a global sequence set with a bias towards a geographic area of interest.

4.46.1. Inputs

4.46.1.1. Required inputs

subsample_by_metadata_with_focal.sample_metadata_tsv
File — Default: None
Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.

subsample_by_metadata_with_focal.sequences_fasta
File — Default: None
Sequences in fasta format.

4.46.1.2. Other inputs

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subsample_by_metadata_with_focal.focal_bin_max
Int — Default: 50
The output will contain no more than this number of focal samples from each discrete value in the focal_bin_variable column.

subsample_by_metadata_with_focal.focal_bin_variable
String — Default: "division"
The focal subset of samples will be evenly subsampled across the discrete values of this column header.

subsample_by_metadata_with_focal.focal_value
String — Default: "North America"
The dataset will be bifurcated based whether the focal_variable column matches this value or not. Rows that match this value are considered to be part of the 'focal' set of interest, rows that do not are part of the 'global' set.

subsample_by_metadata_with_focal.focal_variable
String — Default: "region"
The dataset will be bifurcated based on this column header.

subsample_by_metadata_with_focal.global_bin_max
Int — Default: 50
The output will contain no more than this number of global samples from each discrete value in the global_bin_variable column.

subsample_by_metadata_with_focal.global_bin_variable
String — Default: "country"
The global subset of samples will be evenly subsampled across the discrete values of this column header.

subsample_by_metadata_with_focal.prefilter.docker
String — Default: "nextstrain/base:build-20200629T201240Z"
???

subsample_by_metadata_with_focal.prefilter.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.exclude_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.prefilter.group_by
String? — Default: None
???

subsample_by_metadata_with_focal.prefilter.include
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.prefilter.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.prefilter.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.prefilter.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.prefilter.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.prefilter.priority
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.sequences_per_group
Int? — Default: None
???

subsample_by_metadata_with_focal.prefilter.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal.priorities
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.docker
String — Default: "nextstrain/base:build-20200629T201240Z"
???

subsample_by_metadata_with_focal.subsample_focal.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.include
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.subsample_focal.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.docker
String — Default: "nextstrain/base:build-20200629T201240Z"
???

subsample_by_metadata_with_focal.subsample_global.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.include
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.subsample_global.subsample_seed
Int? — Default: None
???

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