# megablast


## Inputs

### Required inputs
<p name="megablast.blast_db_tgz">
        <b>megablast.blast_db_tgz</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.clipDb">
        <b>megablast.clipDb</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.db_name">
        <b>megablast.db_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.host_species">
        <b>megablast.host_species</b><br />
        <i>Int &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.inBam">
        <b>megablast.inBam</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.taxonomy_db_tgz">
        <b>megablast.taxonomy_db_tgz</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.n_reads">
        <b>megablast.trim_rmdup_subsamp.n_reads</b><br />
        <i>Int &mdash; Default: 10000000</i><br />
        Maximum number of reads set to 10000000 by default.
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="megablast.blastoff.chunkSize">
        <b>megablast.blastoff.chunkSize</b><br />
        <i>Int &mdash; Default: 5000000</i><br />
        ???
</p>
<p name="megablast.blastoff.cpu">
        <b>megablast.blastoff.cpu</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="megablast.blastoff.disk_size_gb">
        <b>megablast.blastoff.disk_size_gb</b><br />
        <i>Int &mdash; Default: 300</i><br />
        ???
</p>
<p name="megablast.blastoff.docker">
        <b>megablast.blastoff.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-classify:fn_blast"</i><br />
        ???
</p>
<p name="megablast.blastoff.fasta_basename">
        <b>megablast.blastoff.fasta_basename</b><br />
        <i>String &mdash; Default: basename(trimmed_fasta,".fasta")</i><br />
        ???
</p>
<p name="megablast.blastoff.log_dir">
        <b>megablast.blastoff.log_dir</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="megablast.blastoff.machine_mem_gb">
        <b>megablast.blastoff.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 64</i><br />
        ???
</p>
<p name="megablast.blastoff.max_target_seqs">
        <b>megablast.blastoff.max_target_seqs</b><br />
        <i>Int &mdash; Default: 50</i><br />
        ???
</p>
<p name="megablast.blastoff.outfmt">
        <b>megablast.blastoff.outfmt</b><br />
        <i>String &mdash; Default: "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue"</i><br />
        ???
</p>
<p name="megablast.blastoff.output_type">
        <b>megablast.blastoff.output_type</b><br />
        <i>String &mdash; Default: "full_line"</i><br />
        ???
</p>
<p name="megablast.blastoff.stage2_min_id">
        <b>megablast.blastoff.stage2_min_id</b><br />
        <i>Int &mdash; Default: 98</i><br />
        ???
</p>
<p name="megablast.blastoff.stage2_min_qcov">
        <b>megablast.blastoff.stage2_min_qcov</b><br />
        <i>Int &mdash; Default: 98</i><br />
        ???
</p>
<p name="megablast.blastoff.stage3_min_id">
        <b>megablast.blastoff.stage3_min_id</b><br />
        <i>Int &mdash; Default: 98</i><br />
        ???
</p>
<p name="megablast.blastoff.stage3_min_qcov">
        <b>megablast.blastoff.stage3_min_qcov</b><br />
        <i>Int &mdash; Default: 98</i><br />
        ???
</p>
<p name="megablast.blastoff.tasks">
        <b>megablast.blastoff.tasks</b><br />
        <i>String &mdash; Default: "megablast"</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.bam_basename">
        <b>megablast.trim_rmdup_subsamp.bam_basename</b><br />
        <i>String &mdash; Default: basename(inBam,'.bam')</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.cpu">
        <b>megablast.trim_rmdup_subsamp.cpu</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.disk_size_gb">
        <b>megablast.trim_rmdup_subsamp.disk_size_gb</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.docker">
        <b>megablast.trim_rmdup_subsamp.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="megablast.trim_rmdup_subsamp.machine_mem_gb">
        <b>megablast.trim_rmdup_subsamp.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 128</i><br />
        ???
</p>
</details>

## Outputs
<p name="megablast.blastoff_kraken">
        <b>megablast.blastoff_kraken</b><br />
        <i>File</i><br />
        ???
</p>
<p name="megablast.blastoff_txt_results">
        <b>megablast.blastoff_txt_results</b><br />
        <i>File</i><br />
        ???
</p>
<p name="megablast.most_popular_taxon_id">
        <b>megablast.most_popular_taxon_id</b><br />
        <i>File</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)