# genbank_single
Prepare assemblies for Genbank submission. This includes annotation by simple coordinate transfer from Genbank annotations and a multiple alignment. See https://viral-pipelines.readthedocs.io/en/latest/ncbi_submission.html for details.

## Inputs

### Required inputs
<p name="genbank_single.assembly_fasta">
        <b>genbank_single.assembly_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        Genome to prepare for Genbank submission. All segments/chromosomes included in one file. Must contain exactly the same number of sequences as reference_accessions.
</p>
<p name="genbank_single.authors_sbt">
        <b>genbank_single.authors_sbt</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.biosample_accession">
        <b>genbank_single.biosample_accession</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.email_address">
        <b>genbank_single.email_address</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.genbank_special_taxa.taxdump_tgz">
        <b>genbank_single.genbank_special_taxa.taxdump_tgz</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.genbank_special_taxa.vadr_by_taxid_tsv">
        <b>genbank_single.genbank_special_taxa.vadr_by_taxid_tsv</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.organism_name">
        <b>genbank_single.organism_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.ref_accessions_colon_delim">
        <b>genbank_single.ref_accessions_colon_delim</b><br />
        <i>String &mdash; Default: None</i><br />
        Reference genome Genbank accessions, each segment/chromosome in the exact same count and order as the segments/chromosomes described in assemblies_fasta. List of accessions should be colon delimited.
</p>
<p name="genbank_single.structured_comments_from_aligned_bam.assembly_method">
        <b>genbank_single.structured_comments_from_aligned_bam.assembly_method</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.structured_comments_from_aligned_bam.assembly_method_version">
        <b>genbank_single.structured_comments_from_aligned_bam.assembly_method_version</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.tax_id">
        <b>genbank_single.tax_id</b><br />
        <i>Int &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="genbank_single.aligned_bam">
        <b>genbank_single.aligned_bam</b><br />
        <i>File? &mdash; Default: None</i><br />
        Normally required: aligned BAM file to inspect for reporting sequencing platform, read depth, etc. in GenBank structured comments.
</p>
<p name="genbank_single.annot.docker">
        <b>genbank_single.annot.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="genbank_single.annot.machine_mem_gb">
        <b>genbank_single.annot.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 30</i><br />
        ???
</p>
<p name="genbank_single.assembly_id">
        <b>genbank_single.assembly_id</b><br />
        <i>String &mdash; Default: basename(basename(basename(assembly_fasta,".fasta"),".fsa"),".fa")</i><br />
        Unique identifier for this assembly. Defaults to the basename of assembly_fasta. table2asn requires this value to be <=50 characters; see: https://www.ncbi.nlm.nih.gov/genbank/table2asn/#fsa
</p>
<p name="genbank_single.biosample_attributes_json">
        <b>genbank_single.biosample_attributes_json</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.biosample_attributes_tsv">
        <b>genbank_single.biosample_attributes_tsv</b><br />
        <i>File? &mdash; Default: None</i><br />
        A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'.
</p>
<p name="genbank_single.biosample_to_genbank.biosample_col_for_fasta_headers">
        <b>genbank_single.biosample_to_genbank.biosample_col_for_fasta_headers</b><br />
        <i>String &mdash; Default: "sample_name"</i><br />
        ???
</p>
<p name="genbank_single.biosample_to_genbank.docker">
        <b>genbank_single.biosample_to_genbank.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="genbank_single.biosample_to_genbank.filter_to_ids">
        <b>genbank_single.biosample_to_genbank.filter_to_ids</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.biosample_to_genbank.isolate_prefix_override">
        <b>genbank_single.biosample_to_genbank.isolate_prefix_override</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.biosample_to_genbank.sanitize_seq_ids">
        <b>genbank_single.biosample_to_genbank.sanitize_seq_ids</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="genbank_single.biosample_to_genbank.src_to_attr_map">
        <b>genbank_single.biosample_to_genbank.src_to_attr_map</b><br />
        <i>Map[String,String] &mdash; Default: {}</i><br />
        ???
</p>
<p name="genbank_single.custom_ref_fsas">
        <b>genbank_single.custom_ref_fsas</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.custom_ref_tbls">
        <b>genbank_single.custom_ref_tbls</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="genbank_single.download_annotations.docker">
        <b>genbank_single.download_annotations.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="genbank_single.fetch_biosamples.docker">
        <b>genbank_single.fetch_biosamples.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/ncbi-tools:2.11.1"</i><br />
        ???
</p>
<p name="genbank_single.genbank_special_taxa.docker">
        <b>genbank_single.genbank_special_taxa.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-classify"</i><br />
        ???
</p>
<p name="genbank_single.structured_comments_from_aligned_bam.docker">
        <b>genbank_single.structured_comments_from_aligned_bam.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="genbank_single.structured_comments_from_aligned_bam.is_genome_assembly">
        <b>genbank_single.structured_comments_from_aligned_bam.is_genome_assembly</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="genbank_single.structured_comments_from_aligned_bam.sanitize_ids">
        <b>genbank_single.structured_comments_from_aligned_bam.sanitize_ids</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="genbank_single.table2asn.comment">
        <b>genbank_single.table2asn.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        Optional comments that can be displayed in the COMMENT section of the Genbank record. This may include any disclaimers about assembly quality or notes about pre-publication availability or requests to discuss pre-publication use with authors.
</p>
<p name="genbank_single.table2asn.docker">
        <b>genbank_single.table2asn.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="genbank_single.table2asn.genetic_code">
        <b>genbank_single.table2asn.genetic_code</b><br />
        <i>Int &mdash; Default: 1</i><br />
        ???
</p>
<p name="genbank_single.table2asn.machine_mem_gb">
        <b>genbank_single.table2asn.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 8</i><br />
        ???
</p>
<p name="genbank_single.table2asn.mol_type">
        <b>genbank_single.table2asn.mol_type</b><br />
        <i>String &mdash; Default: "cRNA"</i><br />
        The type of molecule being described. Any value allowed by the INSDC controlled vocabulary may be used here. Valid values are described at http://www.insdc.org/controlled-vocabulary-moltype-qualifier
</p>
<p name="genbank_single.vadr.cpus">
        <b>genbank_single.vadr.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="genbank_single.vadr.docker">
        <b>genbank_single.vadr.docker</b><br />
        <i>String &mdash; Default: "mirror.gcr.io/staphb/vadr:1.6.4"</i><br />
        ???
</p>
<p name="genbank_single.vadr.minlen">
        <b>genbank_single.vadr.minlen</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
</details>

## Outputs
<p name="genbank_single.annotation_tbl">
        <b>genbank_single.annotation_tbl</b><br />
        <i>File</i><br />
        ???
</p>
<p name="genbank_single.genbank_comment_file">
        <b>genbank_single.genbank_comment_file</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="genbank_single.genbank_file_manifest">
        <b>genbank_single.genbank_file_manifest</b><br />
        <i>String</i><br />
        ???
</p>
<p name="genbank_single.genbank_isolate_name">
        <b>genbank_single.genbank_isolate_name</b><br />
        <i>String</i><br />
        ???
</p>
<p name="genbank_single.genbank_mechanism">
        <b>genbank_single.genbank_mechanism</b><br />
        <i>String</i><br />
        ???
</p>
<p name="genbank_single.genbank_preview_file">
        <b>genbank_single.genbank_preview_file</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="genbank_single.genbank_source_table">
        <b>genbank_single.genbank_source_table</b><br />
        <i>File</i><br />
        ???
</p>
<p name="genbank_single.genbank_submission_sqn">
        <b>genbank_single.genbank_submission_sqn</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="genbank_single.genbank_submit_files">
        <b>genbank_single.genbank_submit_files</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="genbank_single.table2asn_errors">
        <b>genbank_single.table2asn_errors</b><br />
        <i>Array[String]</i><br />
        ???
</p>
<p name="genbank_single.table2asn_pass">
        <b>genbank_single.table2asn_pass</b><br />
        <i>Boolean?</i><br />
        ???
</p>
<p name="genbank_single.table2asn_val_file">
        <b>genbank_single.table2asn_val_file</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="genbank_single.vadr_alerts">
        <b>genbank_single.vadr_alerts</b><br />
        <i>Array[String]</i><br />
        ???
</p>
<p name="genbank_single.vadr_pass">
        <b>genbank_single.vadr_pass</b><br />
        <i>Boolean?</i><br />
        ???
</p>

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