# sarscov2_genbank
Prepare SARS-CoV-2 assemblies for Genbank submission. This includes QC checks with NCBI's VADR tool and filters out genomes that do not pass its tests.

## Inputs

### Required inputs
<p name="sarscov2_genbank.assemblies_fasta">
        <b>sarscov2_genbank.assemblies_fasta</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        Genomes to prepare for Genbank submission. One file per genome: all segments/chromosomes included in one file. All fasta files must contain exactly the same number of sequences as reference_fasta (which must equal the number of files in reference_annot_tbl).
</p>
<p name="sarscov2_genbank.assembly_stats_tsv">
        <b>sarscov2_genbank.assembly_stats_tsv</b><br />
        <i>File &mdash; Default: None</i><br />
        A four column tab text file with one row per sequence and the following header columns: SeqID, Assembly Method, Coverage, Sequencing Technology
</p>
<p name="sarscov2_genbank.author_sbt_defaults_yaml">
        <b>sarscov2_genbank.author_sbt_defaults_yaml</b><br />
        <i>File &mdash; Default: None</i><br />
        A YAML file with default values to use for the submitter, submitter affiliation, and author affiliation. Optionally including authors at the start and end of the author_list. Example: gs://pathogen-public-dbs/other-related/default_sbt_values.yaml
</p>
<p name="sarscov2_genbank.author_sbt_j2_template">
        <b>sarscov2_genbank.author_sbt_j2_template</b><br />
        <i>File &mdash; Default: None</i><br />
        A jinja2-format template for the sbt file expected by NCBI. Example: gs://pathogen-public-dbs/other-related/author_template.sbt.j2
</p>
<p name="sarscov2_genbank.biosample_attributes">
        <b>sarscov2_genbank.biosample_attributes</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="sarscov2_genbank.passing_gisaid_meta.submitting_lab_name">
        <b>sarscov2_genbank.passing_gisaid_meta.submitting_lab_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_package_genbank.account_name">
        <b>sarscov2_genbank.passing_package_genbank.account_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_package_genbank.spuid_namespace">
        <b>sarscov2_genbank.passing_package_genbank.spuid_namespace</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_package_genbank.submission_name">
        <b>sarscov2_genbank.passing_package_genbank.submission_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_package_genbank.submission_uid">
        <b>sarscov2_genbank.passing_package_genbank.submission_uid</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.submitting_lab_name">
        <b>sarscov2_genbank.weird_gisaid_meta.submitting_lab_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_package_genbank.account_name">
        <b>sarscov2_genbank.weird_package_genbank.account_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_package_genbank.spuid_namespace">
        <b>sarscov2_genbank.weird_package_genbank.spuid_namespace</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_package_genbank.submission_name">
        <b>sarscov2_genbank.weird_package_genbank.submission_name</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_package_genbank.submission_uid">
        <b>sarscov2_genbank.weird_package_genbank.submission_uid</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="sarscov2_genbank.assembly_bases.docker">
        <b>sarscov2_genbank.assembly_bases.docker</b><br />
        <i>String &mdash; Default: "ubuntu"</i><br />
        ???
</p>
<p name="sarscov2_genbank.author_list">
        <b>sarscov2_genbank.author_list</b><br />
        <i>String? &mdash; Default: None</i><br />
        A string containing a space-delimited list with of author surnames separated by first name and (optional) middle initial. Ex. 'Lastname,Firstname, Last-hypenated,First,M., Last,F.'
</p>
<p name="sarscov2_genbank.fasta_rename_map">
        <b>sarscov2_genbank.fasta_rename_map</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.generate_author_sbt.docker">
        <b>sarscov2_genbank.generate_author_sbt.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/py3-bio:0.1.2"</i><br />
        ???
</p>
<p name="sarscov2_genbank.generate_author_sbt.out_base">
        <b>sarscov2_genbank.generate_author_sbt.out_base</b><br />
        <i>String &mdash; Default: "authors"</i><br />
        prefix to use for the generated *.sbt output file
</p>
<p name="sarscov2_genbank.gisaid_prefix">
        <b>sarscov2_genbank.gisaid_prefix</b><br />
        <i>String &mdash; Default: 'hCoV-19/'</i><br />
        ???
</p>
<p name="sarscov2_genbank.max_vadr_alerts">
        <b>sarscov2_genbank.max_vadr_alerts</b><br />
        <i>Int &mdash; Default: 0</i><br />
        ???
</p>
<p name="sarscov2_genbank.min_genome_bases">
        <b>sarscov2_genbank.min_genome_bases</b><br />
        <i>Int &mdash; Default: 15000</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_fasta.cpus">
        <b>sarscov2_genbank.passing_fasta.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_gisaid_meta.address_map">
        <b>sarscov2_genbank.passing_gisaid_meta.address_map</b><br />
        <i>String &mdash; Default: '{}'</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_gisaid_meta.authors_map">
        <b>sarscov2_genbank.passing_gisaid_meta.authors_map</b><br />
        <i>String &mdash; Default: '{}'</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_gisaid_meta.continent">
        <b>sarscov2_genbank.passing_gisaid_meta.continent</b><br />
        <i>String &mdash; Default: "North America"</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_gisaid_meta.strict">
        <b>sarscov2_genbank.passing_gisaid_meta.strict</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_gisaid_meta.username">
        <b>sarscov2_genbank.passing_gisaid_meta.username</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_package_genbank.docker">
        <b>sarscov2_genbank.passing_package_genbank.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-baseimage:0.2.0"</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.biosample_col_for_fasta_headers">
        <b>sarscov2_genbank.passing_source_modifiers.biosample_col_for_fasta_headers</b><br />
        <i>String &mdash; Default: "sample_name"</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.docker">
        <b>sarscov2_genbank.passing_source_modifiers.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.filter_to_accession">
        <b>sarscov2_genbank.passing_source_modifiers.filter_to_accession</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.isolate_prefix_override">
        <b>sarscov2_genbank.passing_source_modifiers.isolate_prefix_override</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.organism_name_override">
        <b>sarscov2_genbank.passing_source_modifiers.organism_name_override</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.sanitize_seq_ids">
        <b>sarscov2_genbank.passing_source_modifiers.sanitize_seq_ids</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_source_modifiers.src_to_attr_map">
        <b>sarscov2_genbank.passing_source_modifiers.src_to_attr_map</b><br />
        <i>Map[String,String] &mdash; Default: {}</i><br />
        ???
</p>
<p name="sarscov2_genbank.passing_structured_cmt.docker">
        <b>sarscov2_genbank.passing_structured_cmt.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.4.1"</i><br />
        ???
</p>
<p name="sarscov2_genbank.rename_fasta_header.docker">
        <b>sarscov2_genbank.rename_fasta_header.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.4.1"</i><br />
        ???
</p>
<p name="sarscov2_genbank.rename_fasta_header.out_basename">
        <b>sarscov2_genbank.rename_fasta_header.out_basename</b><br />
        <i>String &mdash; Default: basename(genome_fasta,".fasta")</i><br />
        ???
</p>
<p name="sarscov2_genbank.taxid">
        <b>sarscov2_genbank.taxid</b><br />
        <i>Int &mdash; Default: 2697049</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr.cpus">
        <b>sarscov2_genbank.vadr.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr.docker">
        <b>sarscov2_genbank.vadr.docker</b><br />
        <i>String &mdash; Default: "quay.io/staphb/vadr:1.6.3"</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr.mem_size">
        <b>sarscov2_genbank.vadr.mem_size</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr.vadr_model_tar">
        <b>sarscov2_genbank.vadr.vadr_model_tar</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr.vadr_model_tar_subdir">
        <b>sarscov2_genbank.vadr.vadr_model_tar_subdir</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_fasta.cpus">
        <b>sarscov2_genbank.weird_fasta.cpus</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.address_map">
        <b>sarscov2_genbank.weird_gisaid_meta.address_map</b><br />
        <i>String &mdash; Default: '{}'</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.authors_map">
        <b>sarscov2_genbank.weird_gisaid_meta.authors_map</b><br />
        <i>String &mdash; Default: '{}'</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.continent">
        <b>sarscov2_genbank.weird_gisaid_meta.continent</b><br />
        <i>String &mdash; Default: "North America"</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.strict">
        <b>sarscov2_genbank.weird_gisaid_meta.strict</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta.username">
        <b>sarscov2_genbank.weird_gisaid_meta.username</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_package_genbank.docker">
        <b>sarscov2_genbank.weird_package_genbank.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-baseimage:0.2.0"</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.biosample_col_for_fasta_headers">
        <b>sarscov2_genbank.weird_source_modifiers.biosample_col_for_fasta_headers</b><br />
        <i>String &mdash; Default: "sample_name"</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.docker">
        <b>sarscov2_genbank.weird_source_modifiers.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.filter_to_accession">
        <b>sarscov2_genbank.weird_source_modifiers.filter_to_accession</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.isolate_prefix_override">
        <b>sarscov2_genbank.weird_source_modifiers.isolate_prefix_override</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.organism_name_override">
        <b>sarscov2_genbank.weird_source_modifiers.organism_name_override</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.sanitize_seq_ids">
        <b>sarscov2_genbank.weird_source_modifiers.sanitize_seq_ids</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_source_modifiers.src_to_attr_map">
        <b>sarscov2_genbank.weird_source_modifiers.src_to_attr_map</b><br />
        <i>Map[String,String] &mdash; Default: {}</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_structured_cmt.docker">
        <b>sarscov2_genbank.weird_structured_cmt.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.4.1"</i><br />
        ???
</p>
</details>

## Outputs
<p name="sarscov2_genbank.gisaid_fasta">
        <b>sarscov2_genbank.gisaid_fasta</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.gisaid_meta_csv">
        <b>sarscov2_genbank.gisaid_meta_csv</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.num_input">
        <b>sarscov2_genbank.num_input</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="sarscov2_genbank.num_successful">
        <b>sarscov2_genbank.num_successful</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="sarscov2_genbank.num_weird">
        <b>sarscov2_genbank.num_weird</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="sarscov2_genbank.submission_xml">
        <b>sarscov2_genbank.submission_xml</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.submission_zip">
        <b>sarscov2_genbank.submission_zip</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.submit_ready">
        <b>sarscov2_genbank.submit_ready</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.vadr_outputs">
        <b>sarscov2_genbank.vadr_outputs</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_genbank_xml">
        <b>sarscov2_genbank.weird_genbank_xml</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_genbank_zip">
        <b>sarscov2_genbank.weird_genbank_zip</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_fasta">
        <b>sarscov2_genbank.weird_gisaid_fasta</b><br />
        <i>File</i><br />
        ???
</p>
<p name="sarscov2_genbank.weird_gisaid_meta_csv">
        <b>sarscov2_genbank.weird_gisaid_meta_csv</b><br />
        <i>File</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)