# align_and_count_multiple_report
Count the number of times reads map to provided reference sequences. Useful for counting spike-ins, etc.

## Inputs

### Required inputs
<p name="align_and_count_multiple_report.reads_unmapped_bams">
        <b>align_and_count_multiple_report.reads_unmapped_bams</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        Unaligned reads in BAM format
</p>
<p name="align_and_count_multiple_report.ref_db">
        <b>align_and_count_multiple_report.ref_db</b><br />
        <i>File &mdash; Default: None</i><br />
        File containing sequences against which reads should me aligned and counted
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="align_and_count_multiple_report.align_and_count.docker">
        <b>align_and_count_multiple_report.align_and_count.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.1.33"</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.align_and_count.machine_mem_gb">
        <b>align_and_count_multiple_report.align_and_count.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.align_and_count.topNHits">
        <b>align_and_count_multiple_report.align_and_count.topNHits</b><br />
        <i>Int &mdash; Default: 3</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.align_and_count_summary.docker">
        <b>align_and_count_multiple_report.align_and_count_summary.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.1.33"</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.align_and_count_summary.output_prefix">
        <b>align_and_count_multiple_report.align_and_count_summary.output_prefix</b><br />
        <i>String &mdash; Default: "count_summary"</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.align_and_count_summary_top_hits.docker">
        <b>align_and_count_multiple_report.align_and_count_summary_top_hits.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.1.33"</i><br />
        ???
</p>
</details>

## Outputs
<p name="align_and_count_multiple_report.report">
        <b>align_and_count_multiple_report.report</b><br />
        <i>File</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.report_top_hits">
        <b>align_and_count_multiple_report.report_top_hits</b><br />
        <i>File</i><br />
        ???
</p>
<p name="align_and_count_multiple_report.viral_core_version">
        <b>align_and_count_multiple_report.viral_core_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)