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

## Inputs

### Required inputs
<p name="filter_sequences.filter.sample_metadata_tsv">
        <b>filter_sequences.filter.sample_metadata_tsv</b><br />
        <i>File &mdash; Default: None</i><br />
        Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details.
</p>
<p name="filter_sequences.filter.sequences_fasta">
        <b>filter_sequences.filter.sequences_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="filter_sequences.filter.disk_size">
        <b>filter_sequences.filter.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="filter_sequences.filter.docker">
        <b>filter_sequences.filter.docker</b><br />
        <i>String &mdash; Default: "nextstrain/base:build-20230905T192825Z"</i><br />
        ???
</p>
<p name="filter_sequences.filter.exclude">
        <b>filter_sequences.filter.exclude</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.exclude_where">
        <b>filter_sequences.filter.exclude_where</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.group_by">
        <b>filter_sequences.filter.group_by</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.include">
        <b>filter_sequences.filter.include</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.include_where">
        <b>filter_sequences.filter.include_where</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.max_date">
        <b>filter_sequences.filter.max_date</b><br />
        <i>Float? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.min_date">
        <b>filter_sequences.filter.min_date</b><br />
        <i>Float? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.min_length">
        <b>filter_sequences.filter.min_length</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.non_nucleotide">
        <b>filter_sequences.filter.non_nucleotide</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="filter_sequences.filter.priority">
        <b>filter_sequences.filter.priority</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.sequences_per_group">
        <b>filter_sequences.filter.sequences_per_group</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_sequences.filter.subsample_seed">
        <b>filter_sequences.filter.subsample_seed</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
</details>

## Outputs
<p name="filter_sequences.filter.augur_version">
        <b>filter_sequences.filter.augur_version</b><br />
        <i>String</i><br />
        ???
</p>
<p name="filter_sequences.filter.cpu_load">
        <b>filter_sequences.filter.cpu_load</b><br />
        <i>String</i><br />
        ???
</p>
<p name="filter_sequences.filter.filtered_fasta">
        <b>filter_sequences.filter.filtered_fasta</b><br />
        <i>File</i><br />
        ???
</p>
<p name="filter_sequences.filter.max_ram_gb">
        <b>filter_sequences.filter.max_ram_gb</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="filter_sequences.filter.runtime_sec">
        <b>filter_sequences.filter.runtime_sec</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="filter_sequences.filter.sequences_dropped">
        <b>filter_sequences.filter.sequences_dropped</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="filter_sequences.filter.sequences_out">
        <b>filter_sequences.filter.sequences_out</b><br />
        <i>Int</i><br />
        ???
</p>

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