# scaffold_and_refine_multitaxa
Scaffold de novo contigs against a set of possible references and subsequently polish with reads. This workflow accepts a very large set of input reference genomes. It will subset the reference genomes to those with ANI hits to the provided contigs/MAGs and cluster the reference hits by any ANI similarity to each other. It will choose the top reference from each cluster and produce one assembly for each cluster. This is intended to allow for the presence of multiple diverse viral taxa (coinfections) while forcing a choice of the best assembly from groups of related reference genomes.

## Inputs

### Required inputs
<p name="scaffold_and_refine_multitaxa.contigs_fasta">
        <b>scaffold_and_refine_multitaxa.contigs_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.download_ref_genomes_from_tsv.emailAddress">
        <b>scaffold_and_refine_multitaxa.download_ref_genomes_from_tsv.emailAddress</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.reads_unmapped_bam">
        <b>scaffold_and_refine_multitaxa.reads_unmapped_bam</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.sample_id">
        <b>scaffold_and_refine_multitaxa.sample_id</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.taxid_to_ref_accessions_tsv">
        <b>scaffold_and_refine_multitaxa.taxid_to_ref_accessions_tsv</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>

### Other common inputs
<p name="scaffold_and_refine_multitaxa.refine.trim_coords_bed">
        <b>scaffold_and_refine_multitaxa.refine.trim_coords_bed</b><br />
        <i>File? &mdash; Default: None</i><br />
        optional primers to trim in reference coordinate space (0-based BED format)
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="scaffold_and_refine_multitaxa.refine.call_consensus.mark_duplicates">
        <b>scaffold_and_refine_multitaxa.refine.call_consensus.mark_duplicates</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        Instead of removing duplicates, simply marks them.
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.min_keep_length">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.min_keep_length</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Minimum length of read to retain after trimming (Default: 30)
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.min_quality">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.min_quality</b><br />
        <i>Int? &mdash; Default: 1</i><br />
        Minimum quality threshold for sliding window to pass (Default: 20)
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.sliding_window">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.sliding_window</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Width of sliding window for quality trimming (Default: 4)
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.nucmer_max_gap">
        <b>scaffold_and_refine_multitaxa.scaffold.nucmer_max_gap</b><br />
        <i>Int? &mdash; Default: None</i><br />
        When scaffolding contigs to the reference via nucmer, this specifies the -g parameter to nucmer (the maximum allowed gap between adjacent matches in a cluster). Our default is 200 (up from nucmer default of 90), mummer documentation suggests it is valid to increase up to 1000 to allow for more diversity.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.nucmer_min_cluster">
        <b>scaffold_and_refine_multitaxa.scaffold.nucmer_min_cluster</b><br />
        <i>Int? &mdash; Default: None</i><br />
        When scaffolding contigs to the reference via nucmer, this specifies the -c parameter to nucmer (minimum cluster length). Our default is the nucmer default of 65 bp.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.nucmer_min_match">
        <b>scaffold_and_refine_multitaxa.scaffold.nucmer_min_match</b><br />
        <i>Int? &mdash; Default: None</i><br />
        When scaffolding contigs to the reference via nucmer, this specifies the -l parameter to nucmer (the minimal size of a maximal exact match). Our default is 10 (down from nucmer default of 20) to allow for more divergence.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.replace_length">
        <b>scaffold_and_refine_multitaxa.scaffold.replace_length</b><br />
        <i>Int &mdash; Default: 55</i><br />
        The first and last replace_length base pairs of each segment in the output genome will be replaced with the equivalent sequences in the reference genome as a mechanism to handle common assembly errors in repetitive or inverted regions that are common to chromosome/segment ends. Valid values are any non-negative integer. Default is 55 bp.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.scaffold_min_contig_len">
        <b>scaffold_and_refine_multitaxa.scaffold.scaffold_min_contig_len</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Any sequences in contigs_fasta that are shorter than this length will be ignored for scaffolding.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.scaffold_min_pct_contig_aligned">
        <b>scaffold_and_refine_multitaxa.scaffold.scaffold_min_pct_contig_aligned</b><br />
        <i>Float? &mdash; Default: None</i><br />
        Any contig alignments to the reference scaffold that account for less than this fraction of the contig's length will be rejected for scaffolding. Valid values are fractions from 0 to 1; the default value is 0.3.
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="scaffold_and_refine_multitaxa.assembly_stats_empty.cpus">
        <b>scaffold_and_refine_multitaxa.assembly_stats_empty.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_stats_non_empty.cpus">
        <b>scaffold_and_refine_multitaxa.assembly_stats_non_empty.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.biosample_accession">
        <b>scaffold_and_refine_multitaxa.biosample_accession</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.download_ref_genomes_from_tsv.docker">
        <b>scaffold_and_refine_multitaxa.download_ref_genomes_from_tsv.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref.cpu">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref.docker">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref.read_count_downsample_threshold">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref.read_count_downsample_threshold</b><br />
        <i>Int &mdash; Default: 150000000</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref.sample_name">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref.sample_name</b><br />
        <i>String &mdash; Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_ref_options">
        <b>scaffold_and_refine_multitaxa.refine.align_to_ref_options</b><br />
        <i>Map[String,String] &mdash; Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 501 -k", "bwa": "-k 12 -B 1", "minimap2": ""}</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self.cpu">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self.docker">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self.read_count_downsample_threshold">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self.read_count_downsample_threshold</b><br />
        <i>Int &mdash; Default: 150000000</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self.sample_name">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self.sample_name</b><br />
        <i>String &mdash; Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.align_to_self_options">
        <b>scaffold_and_refine_multitaxa.refine.align_to_self_options</b><br />
        <i>Map[String,String] &mdash; Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": ""}</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.aligner">
        <b>scaffold_and_refine_multitaxa.refine.aligner</b><br />
        <i>String &mdash; Default: "minimap2"</i><br />
        Read aligner software to use. Options: novoalign, bwa, minimap2. Minimap2 can automatically handle Illumina, PacBio, or Oxford Nanopore reads as long as the 'PL' field in the BAM read group header is set properly (novoalign and bwa are Illumina-only).
</p>
<p name="scaffold_and_refine_multitaxa.refine.alignment_metrics.amplicon_set">
        <b>scaffold_and_refine_multitaxa.refine.alignment_metrics.amplicon_set</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.alignment_metrics.docker">
        <b>scaffold_and_refine_multitaxa.refine.alignment_metrics.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.alignment_metrics.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.alignment_metrics.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.alignment_metrics.max_amp_len">
        <b>scaffold_and_refine_multitaxa.refine.alignment_metrics.max_amp_len</b><br />
        <i>Int &mdash; Default: 5000</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.alignment_metrics.max_amplicons">
        <b>scaffold_and_refine_multitaxa.refine.alignment_metrics.max_amplicons</b><br />
        <i>Int &mdash; Default: 500</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.call_consensus.docker">
        <b>scaffold_and_refine_multitaxa.refine.call_consensus.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-assemble"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.call_consensus.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.call_consensus.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.isnvs_ref.docker">
        <b>scaffold_and_refine_multitaxa.refine.isnvs_ref.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.isnvs_ref.out_basename">
        <b>scaffold_and_refine_multitaxa.refine.isnvs_ref.out_basename</b><br />
        <i>String &mdash; Default: basename(aligned_bam,'.bam')</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.isnvs_self.docker">
        <b>scaffold_and_refine_multitaxa.refine.isnvs_self.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.isnvs_self.out_basename">
        <b>scaffold_and_refine_multitaxa.refine.isnvs_self.out_basename</b><br />
        <i>String &mdash; Default: basename(aligned_bam,'.bam')</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.bam_basename">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.bam_basename</b><br />
        <i>String &mdash; Default: basename(aligned_bam,".bam")</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.disk_size">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.disk_size</b><br />
        <i>Int &mdash; Default: 375</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.docker">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.docker</b><br />
        <i>String &mdash; Default: "andersenlabapps/ivar:1.3.1"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.ivar_trim.primer_offset">
        <b>scaffold_and_refine_multitaxa.refine.ivar_trim.primer_offset</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.major_cutoff">
        <b>scaffold_and_refine_multitaxa.refine.major_cutoff</b><br />
        <i>Float &mdash; Default: 0.75</i><br />
        If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position.  If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_ref.disk_size">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_ref.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_ref.docker">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_ref.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_ref.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_ref.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_ref.reheader_table">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_ref.reheader_table</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_self.disk_size">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_self.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_self.docker">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_self.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_self.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_self.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.merge_align_to_self.reheader_table">
        <b>scaffold_and_refine_multitaxa.refine.merge_align_to_self.reheader_table</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.min_coverage">
        <b>scaffold_and_refine_multitaxa.refine.min_coverage</b><br />
        <i>Int &mdash; Default: 3</i><br />
        Minimum read coverage required to call a position unambiguous.
</p>
<p name="scaffold_and_refine_multitaxa.refine.novocraft_license">
        <b>scaffold_and_refine_multitaxa.refine.novocraft_license</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.base_q_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.base_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.bin_large_plots">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.bin_large_plots</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.binning_summary_statistic">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.binning_summary_statistic</b><br />
        <i>String? &mdash; Default: "max"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.docker">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.mapping_q_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.mapping_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.max_coverage_depth">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.max_coverage_depth</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_height_pixels">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_height_pixels</b><br />
        <i>Int? &mdash; Default: 850</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_only_non_duplicates">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_only_non_duplicates</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_pixels_per_inch">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_pixels_per_inch</b><br />
        <i>Int? &mdash; Default: 100</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_width_pixels">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plot_width_pixels</b><br />
        <i>Int? &mdash; Default: 1100</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plotXLimits">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plotXLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plotYLimits">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.plotYLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.read_length_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.read_length_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_ref_coverage.skip_mark_dupes">
        <b>scaffold_and_refine_multitaxa.refine.plot_ref_coverage.skip_mark_dupes</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.base_q_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.base_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.bin_large_plots">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.bin_large_plots</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.binning_summary_statistic">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.binning_summary_statistic</b><br />
        <i>String? &mdash; Default: "max"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.docker">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.mapping_q_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.mapping_q_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.max_coverage_depth">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.max_coverage_depth</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_height_pixels">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_height_pixels</b><br />
        <i>Int? &mdash; Default: 850</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_only_non_duplicates">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_only_non_duplicates</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_pixels_per_inch">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_pixels_per_inch</b><br />
        <i>Int? &mdash; Default: 100</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_width_pixels">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plot_width_pixels</b><br />
        <i>Int? &mdash; Default: 1100</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plotXLimits">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plotXLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.plotYLimits">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.plotYLimits</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.read_length_threshold">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.read_length_threshold</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.plot_self_coverage.skip_mark_dupes">
        <b>scaffold_and_refine_multitaxa.refine.plot_self_coverage.skip_mark_dupes</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.run_discordance.docker">
        <b>scaffold_and_refine_multitaxa.refine.run_discordance.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.sample_original_name">
        <b>scaffold_and_refine_multitaxa.refine.sample_original_name</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.refine.skip_mark_dupes">
        <b>scaffold_and_refine_multitaxa.refine.skip_mark_dupes</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        skip Picard MarkDuplicates step after alignment. This is recommended to be set to true for PCR amplicon based data. (Default: false)
</p>
<p name="scaffold_and_refine_multitaxa.sample_name">
        <b>scaffold_and_refine_multitaxa.sample_name</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.aligner">
        <b>scaffold_and_refine_multitaxa.scaffold.aligner</b><br />
        <i>String &mdash; Default: "muscle"</i><br />
        Alignment tools used to align the reference sequence to aligned contigs. Possible options: muscle, mafft, mummer (= nucmer), set to muscle for default.
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.docker">
        <b>scaffold_and_refine_multitaxa.scaffold.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-assemble"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.scaffold.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.sample_name">
        <b>scaffold_and_refine_multitaxa.scaffold.sample_name</b><br />
        <i>String &mdash; Default: basename(basename(contigs_fasta,".fasta"),".assembly1-spades")</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.skani_c">
        <b>scaffold_and_refine_multitaxa.scaffold.skani_c</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.skani_m">
        <b>scaffold_and_refine_multitaxa.scaffold.skani_m</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.scaffold.skani_s">
        <b>scaffold_and_refine_multitaxa.scaffold.skani_s</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.cpu">
        <b>scaffold_and_refine_multitaxa.select_references.cpu</b><br />
        <i>Int &mdash; Default: 2</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.disk_size">
        <b>scaffold_and_refine_multitaxa.select_references.disk_size</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.docker">
        <b>scaffold_and_refine_multitaxa.select_references.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-assemble"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.machine_mem_gb">
        <b>scaffold_and_refine_multitaxa.select_references.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.skani_c">
        <b>scaffold_and_refine_multitaxa.select_references.skani_c</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.skani_m">
        <b>scaffold_and_refine_multitaxa.select_references.skani_m</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.skani_n">
        <b>scaffold_and_refine_multitaxa.select_references.skani_n</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.select_references.skani_s">
        <b>scaffold_and_refine_multitaxa.select_references.skani_s</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.table_name">
        <b>scaffold_and_refine_multitaxa.table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.tar_extract.disk_size">
        <b>scaffold_and_refine_multitaxa.tar_extract.disk_size</b><br />
        <i>Int &mdash; Default: 375</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.tar_extract.tar_opts">
        <b>scaffold_and_refine_multitaxa.tar_extract.tar_opts</b><br />
        <i>String &mdash; Default: "-z"</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.tax_lookup.set_default_keys">
        <b>scaffold_and_refine_multitaxa.tax_lookup.set_default_keys</b><br />
        <i>Array[String] &mdash; Default: []</i><br />
        ???
</p>
</details>

## Outputs
<p name="scaffold_and_refine_multitaxa.assembly_all_fastas">
        <b>scaffold_and_refine_multitaxa.assembly_all_fastas</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_all_lengths_unambig">
        <b>scaffold_and_refine_multitaxa.assembly_all_lengths_unambig</b><br />
        <i>Array[Int]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_all_pct_ref_cov">
        <b>scaffold_and_refine_multitaxa.assembly_all_pct_ref_cov</b><br />
        <i>Array[Float]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_all_taxids">
        <b>scaffold_and_refine_multitaxa.assembly_all_taxids</b><br />
        <i>Array[String]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_all_taxnames">
        <b>scaffold_and_refine_multitaxa.assembly_all_taxnames</b><br />
        <i>Array[String]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_method">
        <b>scaffold_and_refine_multitaxa.assembly_method</b><br />
        <i>String</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_stats_by_taxon">
        <b>scaffold_and_refine_multitaxa.assembly_stats_by_taxon</b><br />
        <i>Array[Map[String,String]]</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.assembly_stats_by_taxon_tsv">
        <b>scaffold_and_refine_multitaxa.assembly_stats_by_taxon_tsv</b><br />
        <i>File</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.skani_contigs_to_refs_dist_tsv">
        <b>scaffold_and_refine_multitaxa.skani_contigs_to_refs_dist_tsv</b><br />
        <i>File</i><br />
        ???
</p>
<p name="scaffold_and_refine_multitaxa.skani_num_ref_clusters">
        <b>scaffold_and_refine_multitaxa.skani_num_ref_clusters</b><br />
        <i>Int</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)