# deplete_only
Taxonomic depletion of reads matching unwanted taxa (such as human).

## Inputs

### Required inputs
<p name="deplete_only.deplete_taxa.raw_reads_unmapped_bam">
        <b>deplete_only.deplete_taxa.raw_reads_unmapped_bam</b><br />
        <i>File &mdash; Default: None</i><br />
        unaligned reads in BAM format
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="deplete_only.deplete_taxa.blastDbs">
        <b>deplete_only.deplete_taxa.blastDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.
</p>
<p name="deplete_only.deplete_taxa.bmtaggerDbs">
        <b>deplete_only.deplete_taxa.bmtaggerDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
</p>
<p name="deplete_only.deplete_taxa.bwaDbs">
        <b>deplete_only.deplete_taxa.bwaDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.
</p>
<p name="deplete_only.deplete_taxa.clear_tags">
        <b>deplete_only.deplete_taxa.clear_tags</b><br />
        <i>Boolean? &mdash; Default: false</i><br />
        ???
</p>
<p name="deplete_only.deplete_taxa.cpu">
        <b>deplete_only.deplete_taxa.cpu</b><br />
        <i>Int? &mdash; Default: 8</i><br />
        ???
</p>
<p name="deplete_only.deplete_taxa.docker">
        <b>deplete_only.deplete_taxa.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"</i><br />
        ???
</p>
<p name="deplete_only.deplete_taxa.machine_mem_gb">
        <b>deplete_only.deplete_taxa.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="deplete_only.deplete_taxa.query_chunk_size">
        <b>deplete_only.deplete_taxa.query_chunk_size</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="deplete_only.deplete_taxa.tags_to_clear_space_separated">
        <b>deplete_only.deplete_taxa.tags_to_clear_space_separated</b><br />
        <i>String? &mdash; Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"</i><br />
        ???
</p>
</details>

## Outputs
<p name="deplete_only.cleaned_bam">
        <b>deplete_only.cleaned_bam</b><br />
        <i>File</i><br />
        ???
</p>
<p name="deplete_only.cleaned_fastqc">
        <b>deplete_only.cleaned_fastqc</b><br />
        <i>File</i><br />
        ???
</p>
<p name="deplete_only.cleaned_fastqc_zip">
        <b>deplete_only.cleaned_fastqc_zip</b><br />
        <i>File</i><br />
        ???
</p>
<p name="deplete_only.depletion_read_count_post">
        <b>deplete_only.depletion_read_count_post</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="deplete_only.depletion_read_count_pre">
        <b>deplete_only.depletion_read_count_pre</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="deplete_only.viral_classify_version">
        <b>deplete_only.viral_classify_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)