4.38. genbank¶
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.
4.38.1. Inputs¶
4.38.1.1. Required inputs¶
genbank.alignments_bams
Array[File] — Default: None
???
genbank.assemblies_fasta
Array[File]+ — Default: None
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).
genbank.author_sbt_defaults_yaml
File — Default: None
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
genbank.author_sbt_j2_template
File — Default: None
A jinja2-format template for the sbt file expected by NCBI. Example: gs://pathogen-public-dbs/other-related/author_template.sbt.j2
genbank.biosample_attributes
File — Default: None
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'.
genbank.email_address
String — Default: None
???
genbank.reference_accessions
Array[String]+ — Default: None
Reference genome Genbank accessions, each segment/chromosome in the exact same count and order as the segments/chromosomes described in assemblies_fasta.
genbank.sequencingTech
String — Default: None
The type of sequencer used to generate reads. NCBI has a controlled vocabulary for this value which can be found here: https://submit.ncbi.nlm.nih.gov/structcomment/nongenomes/
4.38.1.2. Other common inputs¶
genbank.coverage_table
File? — Default: None
A two column tab text file mapping sample IDs (first column) to average sequencing coverage (second column, floating point number).
genbank.molType
String — Default: 'cRNA'
The type of molecule being described. This defaults to 'cRNA' as this pipeline is most commonly used for viral submissions, but 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
4.38.1.3. Other inputs¶
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genbank.annot.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
genbank.author_list
String? — Default: None
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.'
genbank.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
genbank.biosample_to_genbank.filter_to_ids
File? — Default: None
???
genbank.comment
String? — Default: None
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.
genbank.coverage_report.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
genbank.coverage_report.out_report_name
String — Default: "coverage_report.txt"
???
genbank.coverage_two_col.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
genbank.coverage_two_col.out_filename
String — Default: basename(in_tsv,'.tsv') + ".drop.tsv"
???
genbank.download_annotations.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
genbank.fetch_genbank_metadata.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???
genbank.generate_author_sbt.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
genbank.generate_author_sbt.out_base
String? — Default: "authors"
prefix to use for the generated *.sbt output file
genbank.prep_genbank.assembly_method
String? — Default: None
Very short description of the software approach used to assemble the genome. We typically provide a github link here. If this is specified, assembly_method_version should also be specified.
genbank.prep_genbank.assembly_method_version
String? — Default: None
The version of the software used. If this is specified, assembly_method should also be specified.
genbank.prep_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
genbank.prep_genbank.machine_mem_gb
Int? — Default: None
???
4.38.2. Outputs¶
genbank.archive_zip
File
???
genbank.biosample_map
File
???
genbank.errorSummary
File
???
genbank.genbank_preview_files
Array[File]
???
genbank.genbank_source_table
File
???
genbank.submission_zip
File
???
genbank.transferred_annot_tbls
Array[File]
???
genbank.validation_files
Array[File]
???
genbank.viral_phylo_version
String
???
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