4.37. filter_sequences

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

4.37.1. Inputs

4.37.1.1. Required inputs

filter_sequences.filter.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.

filter_sequences.filter.sequences_fasta
File — Default: None
Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.

4.37.1.2. Other inputs

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filter_sequences.filter.disk_size
Int — Default: 750
???

filter_sequences.filter.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

filter_sequences.filter.exclude
File? — Default: None
???

filter_sequences.filter.exclude_where
Array[String]? — Default: None
???

filter_sequences.filter.group_by
String? — Default: None
???

filter_sequences.filter.include
File? — Default: None
???

filter_sequences.filter.include_where
Array[String]? — Default: None
???

filter_sequences.filter.max_date
Float? — Default: None
???

filter_sequences.filter.min_date
Float? — Default: None
???

filter_sequences.filter.min_length
Int? — Default: None
???

filter_sequences.filter.non_nucleotide
Boolean — Default: true
???

filter_sequences.filter.priority
File? — Default: None
???

filter_sequences.filter.sequences_per_group
Int? — Default: None
???

filter_sequences.filter.subsample_seed
Int? — Default: None
???

4.37.2. Outputs

filter_sequences.filter.augur_version
String
???

filter_sequences.filter.cpu_load
String
???

filter_sequences.filter.filtered_fasta
File
???

filter_sequences.filter.max_ram_gb
Int
???

filter_sequences.filter.runtime_sec
Int
???

filter_sequences.filter.sequences_dropped
Int
???

filter_sequences.filter.sequences_out
Int
???

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