# filter_classified_bam_to_taxa
Taxonomic filtration of reads utilizing output from a classifier such as kraken1/2/uniq. Can filter out or filter to a specified taxonomic grouping.

## Inputs

### Required inputs
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_bam">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_bam</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_reads_txt_gz">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_reads_txt_gz</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.ncbi_taxonomy_db_tgz">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.ncbi_taxonomy_db_tgz</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.docker">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.exclude_taxa">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.exclude_taxa</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.machine_mem_gb">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.minimum_hit_groups">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.minimum_hit_groups</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.out_filename_suffix">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.out_filename_suffix</b><br />
        <i>String &mdash; Default: "filtered"</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_ids">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_ids</b><br />
        <i>Array[Int]? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_names">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_names</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.filter_bam_to_taxa.withoutChildren">
        <b>filter_classified_bam_to_taxa.filter_bam_to_taxa.withoutChildren</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
</details>

## Outputs
<p name="filter_classified_bam_to_taxa.bam_filtered_to_taxa">
        <b>filter_classified_bam_to_taxa.bam_filtered_to_taxa</b><br />
        <i>File</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_post">
        <b>filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_post</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_pre">
        <b>filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_pre</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="filter_classified_bam_to_taxa.viral_classify_version">
        <b>filter_classified_bam_to_taxa.viral_classify_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)