# pairwise_distances
Download genomes by accession, compute pairwise distances with skani, and optionally generate MSA and tree

## Inputs

### Required inputs
<p name="pairwise_distances.accessions_file">
        <b>pairwise_distances.accessions_file</b><br />
        <i>File &mdash; Default: None</i><br />
        Text file with GenBank accession numbers for single segment genomes, one per line
</p>
<p name="pairwise_distances.emailAddress">
        <b>pairwise_distances.emailAddress</b><br />
        <i>String &mdash; Default: None</i><br />
        Email address for NCBI Entrez identification
</p>

### Other common inputs
<p name="pairwise_distances.make_tree">
        <b>pairwise_distances.make_tree</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        If true, generate multiple sequence alignment and phylogenetic tree in addition to pairwise distances
</p>
<p name="pairwise_distances.out_prefix">
        <b>pairwise_distances.out_prefix</b><br />
        <i>String &mdash; Default: "pairwise_dist"</i><br />
        Prefix for output file names
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="pairwise_distances.skani_triangle.compression_factor">
        <b>pairwise_distances.skani_triangle.compression_factor</b><br />
        <i>Int &mdash; Default: 10</i><br />
        Compression factor for skani (-c parameter, default 10)
</p>
<p name="pairwise_distances.skani_triangle.marker_compression">
        <b>pairwise_distances.skani_triangle.marker_compression</b><br />
        <i>Int &mdash; Default: 15</i><br />
        Marker compression factor for skani (-m parameter, default 15)
</p>
<p name="pairwise_distances.skani_triangle.min_aligned_frac">
        <b>pairwise_distances.skani_triangle.min_aligned_frac</b><br />
        <i>Int &mdash; Default: 15</i><br />
        Minimum aligned fraction for skani (--min-af parameter, default 15)
</p>
<p name="pairwise_distances.skani_triangle.sketch_size">
        <b>pairwise_distances.skani_triangle.sketch_size</b><br />
        <i>Int &mdash; Default: 50</i><br />
        Sketch size parameter for skani (-s parameter, default 50)
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="pairwise_distances.download_fasta.docker">
        <b>pairwise_distances.download_fasta.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.cpus">
        <b>pairwise_distances.draft_augur_tree.cpus</b><br />
        <i>Int &mdash; Default: 64</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.disk_size">
        <b>pairwise_distances.draft_augur_tree.disk_size</b><br />
        <i>Int &mdash; Default: 1250</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.docker">
        <b>pairwise_distances.draft_augur_tree.docker</b><br />
        <i>String &mdash; Default: "docker.io/nextstrain/base:build-20240318T173028Z"</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.exclude_sites">
        <b>pairwise_distances.draft_augur_tree.exclude_sites</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.machine_mem_gb">
        <b>pairwise_distances.draft_augur_tree.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 32</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.method">
        <b>pairwise_distances.draft_augur_tree.method</b><br />
        <i>String &mdash; Default: "iqtree"</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.substitution_model">
        <b>pairwise_distances.draft_augur_tree.substitution_model</b><br />
        <i>String &mdash; Default: "GTR"</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.tree_builder_args">
        <b>pairwise_distances.draft_augur_tree.tree_builder_args</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="pairwise_distances.draft_augur_tree.vcf_reference">
        <b>pairwise_distances.draft_augur_tree.vcf_reference</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.cpus">
        <b>pairwise_distances.mafft_one_chr.cpus</b><br />
        <i>Int &mdash; Default: 64</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.disk_size">
        <b>pairwise_distances.mafft_one_chr.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.docker">
        <b>pairwise_distances.mafft_one_chr.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.keep_length">
        <b>pairwise_distances.mafft_one_chr.keep_length</b><br />
        <i>Boolean? &mdash; Default: None</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.large">
        <b>pairwise_distances.mafft_one_chr.large</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.mem_size">
        <b>pairwise_distances.mafft_one_chr.mem_size</b><br />
        <i>Int &mdash; Default: 500</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.memsavetree">
        <b>pairwise_distances.mafft_one_chr.memsavetree</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.ref_fasta">
        <b>pairwise_distances.mafft_one_chr.ref_fasta</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="pairwise_distances.mafft_one_chr.remove_reference">
        <b>pairwise_distances.mafft_one_chr.remove_reference</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="pairwise_distances.skani_triangle.cpu">
        <b>pairwise_distances.skani_triangle.cpu</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="pairwise_distances.skani_triangle.disk_size">
        <b>pairwise_distances.skani_triangle.disk_size</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="pairwise_distances.skani_triangle.docker">
        <b>pairwise_distances.skani_triangle.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-assemble"</i><br />
        ???
</p>
<p name="pairwise_distances.skani_triangle.machine_mem_gb">
        <b>pairwise_distances.skani_triangle.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
</details>

## Outputs
<p name="pairwise_distances.iqtree_nwk">
        <b>pairwise_distances.iqtree_nwk</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="pairwise_distances.msa_fasta">
        <b>pairwise_distances.msa_fasta</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="pairwise_distances.pairwise_dist_skani">
        <b>pairwise_distances.pairwise_dist_skani</b><br />
        <i>File</i><br />
        ???
</p>
<p name="pairwise_distances.sequences_fasta">
        <b>pairwise_distances.sequences_fasta</b><br />
        <i>File</i><br />
        ???
</p>

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