# isnvs_lofreq
variant calls by LoFreq against reference_fasta

## Inputs

### Required inputs
<p name="isnvs_lofreq.aligned_bams">
        <b>isnvs_lofreq.aligned_bams</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        reads aligned to the sequence within reference_fasta.
</p>
<p name="isnvs_lofreq.reference_fasta">
        <b>isnvs_lofreq.reference_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        Reference sequence to which reads have be aligned
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="isnvs_lofreq.lofreq.docker">
        <b>isnvs_lofreq.lofreq.docker</b><br />
        <i>String &mdash; Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"</i><br />
        ???
</p>
<p name="isnvs_lofreq.lofreq.out_basename">
        <b>isnvs_lofreq.lofreq.out_basename</b><br />
        <i>String &mdash; Default: basename(aligned_bam,'.bam')</i><br />
        ???
</p>
</details>

## Outputs
<p name="isnvs_lofreq.lofreq_vcfs">
        <b>isnvs_lofreq.lofreq_vcfs</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="isnvs_lofreq.lofreq_version">
        <b>isnvs_lofreq.lofreq_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)