# mafft
MAFFT multiple-alignment for a set of possibly multi-segment genomes.

## Inputs

### Required inputs
<p name="mafft.multi_align_mafft_ref.assemblies_fasta">
        <b>mafft.multi_align_mafft_ref.assemblies_fasta</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        ???
</p>
<p name="mafft.multi_align_mafft_ref.reference_fasta">
        <b>mafft.multi_align_mafft_ref.reference_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="mafft.multi_align_mafft_ref.docker">
        <b>mafft.multi_align_mafft_ref.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-phylo:2.5.1.0"</i><br />
        ???
</p>
<p name="mafft.multi_align_mafft_ref.machine_mem_gb">
        <b>mafft.multi_align_mafft_ref.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="mafft.multi_align_mafft_ref.mafft_ep">
        <b>mafft.multi_align_mafft_ref.mafft_ep</b><br />
        <i>Float? &mdash; Default: None</i><br />
        ???
</p>
<p name="mafft.multi_align_mafft_ref.mafft_gapOpeningPenalty">
        <b>mafft.multi_align_mafft_ref.mafft_gapOpeningPenalty</b><br />
        <i>Float? &mdash; Default: None</i><br />
        ???
</p>
<p name="mafft.multi_align_mafft_ref.mafft_maxIters">
        <b>mafft.multi_align_mafft_ref.mafft_maxIters</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
</details>

## Outputs
<p name="mafft.alignments_by_chr">
        <b>mafft.alignments_by_chr</b><br />
        <i>Array[File]</i><br />
        ???
</p>

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> Generated using WDL AID (1.0.0)