# merge_metagenomics
Combine metagenomic reports from single samples into an aggregate report.

## Inputs

### Required inputs
<p name="merge_metagenomics.krakenuniq_summary_reports">
        <b>merge_metagenomics.krakenuniq_summary_reports</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>
<p name="merge_metagenomics.krona_per_sample">
        <b>merge_metagenomics.krona_per_sample</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxlevel_focus">
        <b>merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxlevel_focus</b><br />
        <i>String &mdash; Default: "species"</i><br />
        species,genus,family,order,class,phylum,kingdom,superkingdom
</p>
<p name="merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxon_heading_space_separated">
        <b>merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxon_heading_space_separated</b><br />
        <i>String &mdash; Default: "Viruses"</i><br />
        The taxonomic heading to analyze. More than one can be specified.
</p>
<p name="merge_metagenomics.aggregate_metagenomics_reports.aggregate_top_N_hits">
        <b>merge_metagenomics.aggregate_metagenomics_reports.aggregate_top_N_hits</b><br />
        <i>Int &mdash; Default: 5</i><br />
        only include the top N hits from a given sample in the aggregate report
</p>
<p name="merge_metagenomics.aggregate_metagenomics_reports.docker">
        <b>merge_metagenomics.aggregate_metagenomics_reports.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"</i><br />
        ???
</p>
<p name="merge_metagenomics.krona_merge.docker">
        <b>merge_metagenomics.krona_merge.docker</b><br />
        <i>String &mdash; Default: "biocontainers/krona:v2.7.1_cv1"</i><br />
        ???
</p>
<p name="merge_metagenomics.krona_merge.machine_mem_gb">
        <b>merge_metagenomics.krona_merge.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
</details>

## Outputs
<p name="merge_metagenomics.krona_merged">
        <b>merge_metagenomics.krona_merged</b><br />
        <i>File</i><br />
        ???
</p>
<p name="merge_metagenomics.metagenomics_summary">
        <b>merge_metagenomics.metagenomics_summary</b><br />
        <i>File</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)