4.38. subsample_by_metadata

Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html

4.38.1. Inputs

4.38.1.1. Required inputs

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

subsample_by_metadata.filter_subsample_sequences.sequences_fasta
File — Default: None
Set of sequences in fasta format to subsample using augur filter. These must represent a single chromosome/segment of a genome only.

4.38.1.2. Other inputs

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subsample_by_metadata.filter_subsample_sequences.docker
String — Default: "nextstrain/base"
???

subsample_by_metadata.filter_subsample_sequences.exclude
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.exclude_where
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.group_by
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.include
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.include_where
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.machine_mem_gb
Int? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.max_date
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.min_date
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.min_length
Int? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata.filter_subsample_sequences.priority
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.sequences_per_group
Int? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.subsample_seed
Int? — Default: None
???

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