# reconstruct_from_alignments
Infer disease transmission events from sequence (consensus + intrahost variation) data using the reconstructR tool

## Inputs

### Required inputs
<p name="reconstruct_from_alignments.aligned_trimmed_bams">
        <b>reconstruct_from_alignments.aligned_trimmed_bams</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.assembly_fastas">
        <b>reconstruct_from_alignments.assembly_fastas</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.date_csv">
        <b>reconstruct_from_alignments.reconstructr.date_csv</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.n_iters">
        <b>reconstruct_from_alignments.reconstructr.n_iters</b><br />
        <i>Int &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.ref_fasta">
        <b>reconstruct_from_alignments.ref_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="reconstruct_from_alignments.get_bam_samplename.docker">
        <b>reconstruct_from_alignments.get_bam_samplename.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.isnvs_ref.docker">
        <b>reconstruct_from_alignments.isnvs_ref.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.cpus">
        <b>reconstruct_from_alignments.mafft.cpus</b><br />
        <i>Int &mdash; Default: 64</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.disk_size">
        <b>reconstruct_from_alignments.mafft.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.docker">
        <b>reconstruct_from_alignments.mafft.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.keep_length">
        <b>reconstruct_from_alignments.mafft.keep_length</b><br />
        <i>Boolean? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.large">
        <b>reconstruct_from_alignments.mafft.large</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.mem_size">
        <b>reconstruct_from_alignments.mafft.mem_size</b><br />
        <i>Int &mdash; Default: 500</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.mafft.memsavetree">
        <b>reconstruct_from_alignments.mafft.memsavetree</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.merge_coverage_per_position.disk_size">
        <b>reconstruct_from_alignments.merge_coverage_per_position.disk_size</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.merge_coverage_per_position.docker">
        <b>reconstruct_from_alignments.merge_coverage_per_position.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/py3-bio:0.1.3"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.merge_coverage_per_position.out_report_name">
        <b>reconstruct_from_alignments.merge_coverage_per_position.out_report_name</b><br />
        <i>String &mdash; Default: "coverage_report.csv"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.base_q_threshold">
        <b>reconstruct_from_alignments.plot_ref_coverage.base_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.bin_large_plots">
        <b>reconstruct_from_alignments.plot_ref_coverage.bin_large_plots</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.binning_summary_statistic">
        <b>reconstruct_from_alignments.plot_ref_coverage.binning_summary_statistic</b><br />
        <i>String? &mdash; Default: "max"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.docker">
        <b>reconstruct_from_alignments.plot_ref_coverage.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.mapping_q_threshold">
        <b>reconstruct_from_alignments.plot_ref_coverage.mapping_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.max_coverage_depth">
        <b>reconstruct_from_alignments.plot_ref_coverage.max_coverage_depth</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plot_height_pixels">
        <b>reconstruct_from_alignments.plot_ref_coverage.plot_height_pixels</b><br />
        <i>Int? &mdash; Default: 850</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plot_only_non_duplicates">
        <b>reconstruct_from_alignments.plot_ref_coverage.plot_only_non_duplicates</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plot_pixels_per_inch">
        <b>reconstruct_from_alignments.plot_ref_coverage.plot_pixels_per_inch</b><br />
        <i>Int? &mdash; Default: 100</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plot_width_pixels">
        <b>reconstruct_from_alignments.plot_ref_coverage.plot_width_pixels</b><br />
        <i>Int? &mdash; Default: 1100</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plotXLimits">
        <b>reconstruct_from_alignments.plot_ref_coverage.plotXLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.plotYLimits">
        <b>reconstruct_from_alignments.plot_ref_coverage.plotYLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.read_length_threshold">
        <b>reconstruct_from_alignments.plot_ref_coverage.read_length_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.plot_ref_coverage.skip_mark_dupes">
        <b>reconstruct_from_alignments.plot_ref_coverage.skip_mark_dupes</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.cpus">
        <b>reconstruct_from_alignments.reconstructr.cpus</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.disk_size">
        <b>reconstruct_from_alignments.reconstructr.disk_size</b><br />
        <i>Int &mdash; Default: 375</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.docker">
        <b>reconstruct_from_alignments.reconstructr.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/reconstructr:main"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.machine_mem_gb">
        <b>reconstruct_from_alignments.reconstructr.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 15</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr.out_basename">
        <b>reconstruct_from_alignments.reconstructr.out_basename</b><br />
        <i>String &mdash; Default: "reconstructR"</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.zcat.cpus">
        <b>reconstruct_from_alignments.zcat.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
</details>

## Outputs
<p name="reconstruct_from_alignments.depth_csv">
        <b>reconstruct_from_alignments.depth_csv</b><br />
        <i>File</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.lofreq_isnvs">
        <b>reconstruct_from_alignments.lofreq_isnvs</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.msa_fasta">
        <b>reconstruct_from_alignments.msa_fasta</b><br />
        <i>File</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr_deciphered_tsv_gz">
        <b>reconstruct_from_alignments.reconstructr_deciphered_tsv_gz</b><br />
        <i>File</i><br />
        ???
</p>
<p name="reconstruct_from_alignments.reconstructr_tabulated_tsv_gz">
        <b>reconstruct_from_alignments.reconstructr_tabulated_tsv_gz</b><br />
        <i>File</i><br />
        ???
</p>

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