4.70. subsample_by_metadata¶
Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html
4.70.1. Inputs¶
4.70.1.1. 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 (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.
4.70.1.2. Other inputs¶
Show/Hide
subsample_by_metadata.filter_subsample_sequences.disk_size
Int — Default: 750
???
subsample_by_metadata.filter_subsample_sequences.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
subsample_by_metadata.filter_subsample_sequences.exclude
File? — Default: None
???
subsample_by_metadata.filter_subsample_sequences.exclude_where
Array[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
Array[String]? — Default: None
???
subsample_by_metadata.filter_subsample_sequences.max_date
Float? — Default: None
???
subsample_by_metadata.filter_subsample_sequences.min_date
Float? — 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
???
4.70.2. Outputs¶
subsample_by_metadata.filtered_fasta
File
???
Generated using WDL AID (1.0.0)